revdep/problems.md

In HenrikBengtsson/R.utils: Various Programming Utilities

acroname

• Version: 0.1.0
• GitHub: NA
• Source code: https://github.com/cran/acroname
• Date/Publication: 2021-01-25 08:40:11 UTC
• Number of recursive dependencies: 52

Run revdep_details(, "acroname") for more info

In both

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘hunspell’ All declared Imports should be used.

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

adjustedCurves

• Version: 0.9.0
• GitHub: https://github.com/RobinDenz1/adjustedCurves
• Source code: https://github.com/cran/adjustedCurves
• Date/Publication: 2022-09-22 08:40:13 UTC
• Number of recursive dependencies: 166

Run revdep_details(, "adjustedCurves") for more info

In both

• checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'cif_aiptw.Rd': ‘coxph’

  Missing link or links in documentation object 'cif_aiptw_pseudo.Rd': ‘multinom’

  Missing link or links in documentation object 'cif_iptw.Rd': ‘multinom’

  Missing link or links in documentation object 'cif_iptw_pseudo.Rd': ... Missing link or links in documentation object 'surv_iptw_km.Rd': ‘multinom’

  Missing link or links in documentation object 'surv_iptw_pseudo.Rd': ‘multinom’

  Missing link or links in documentation object 'surv_km.Rd': ‘survfit’

  See section 'Cross-references' in the 'Writing R Extensions' manual. ```

affxparser

• Version: 1.68.1
• GitHub: https://github.com/HenrikBengtsson/affxparser
• Source code: https://github.com/cran/affxparser
• Date/Publication: 2022-04-29
• Number of recursive dependencies: 4

Run revdep_details(, "affxparser") for more info

In both

• checking whether package ‘affxparser’ can be installed ... WARNING Found the following significant warnings: fusion/file/CELFileData.cpp:2409:27: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2414:27: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2419:28: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2445:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2451:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2457:38: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2506:23: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2509:23: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2512:24: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2551:24: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:2554:24: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:3194:16: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:3199:16: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:3204:17: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:3251:17: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:3255:16: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] fusion/file/CELFileData.cpp:3294:28: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] See ‘/c4/home/henrik/repositories/R.utils/revdep/checks/affxparser/new/affxparser.Rcheck/00install.out’ for details.

• checking compiled code ... WARNING ``` File ‘affxparser/libs/affxparser.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Object: ‘fusion/util/Verbose.o’ Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Objects: ‘fusion/file/TsvFile/TsvFile.o’, ‘fusion/util/Err.o’ Found ‘abort’, possibly from ‘abort’ (C) Objects: ‘fusion/calvin_files/fusion/src/FusionCHPData.o’, ‘fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o’, ‘fusion/calvin_files/parameter/src/ParameterNameValueType.o’, ‘fusion/file/BPMAPFileWriter.o’ ... Found ‘srand’, possibly from ‘srand’ (C) Object: ‘fusion/calvin_files/utils/src/AffymetrixGuid.o’ Found ‘stdout’, possibly from ‘stdout’ (C) Object: ‘fusion/util/Util.o’

  Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs.

  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

• checking installed package size ... NOTE installed size is 18.0Mb sub-directories of 1Mb or more: libs 17.5Mb

• checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘affy’

arc

• Version: 1.3
• GitHub: https://github.com/kliegr/arc
• Source code: https://github.com/cran/arc
• Date/Publication: 2020-11-07 00:20:11 UTC
• Number of recursive dependencies: 10

Run revdep_details(, "arc") for more info

In both

• checking package dependencies ... NOTE Package suggested but not available for checking: ‘qCBA’

aroma.core

• Version: 3.2.2
• GitHub: https://github.com/HenrikBengtsson/aroma.core
• Source code: https://github.com/cran/aroma.core
• Date/Publication: 2021-01-05 05:10:12 UTC
• Number of recursive dependencies: 48

Run revdep_details(, "aroma.core") for more info

In both

• checking package dependencies ... NOTE Packages suggested but not available for checking: 'sfit', 'expectile', 'HaarSeg', 'mpcbs'

aroma.light

• Version: 3.26.0
• GitHub: https://github.com/HenrikBengtsson/aroma.light
• Source code: https://github.com/cran/aroma.light
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 6

Run revdep_details(, "aroma.light") for more info

In both

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: inst/rsp/.rspPlugins These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

AUCell

• Version: 1.18.1
• GitHub: NA
• Source code: https://github.com/cran/AUCell
• Date/Publication: 2022-05-19
• Number of recursive dependencies: 170

Run revdep_details(, "AUCell") for more info

In both

• checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'doMC', 'doRNG'

• checking R code for possible problems ... NOTE AUCell_createViewerApp : <anonymous>: no visible global function definition for ‘%>%’ AUCell_createViewerApp : <anonymous>: no visible binding for global variable ‘tsne1’ AUCell_createViewerApp : <anonymous>: no visible binding for global variable ‘tsne2’ AUCell_createViewerApp : <anonymous>: no visible binding for global variable ‘cell’ plotEmb_rgb : <anonymous>: no visible global function definition for ‘rgb’ Undefined global functions or variables: %>% cell rgb tsne1 tsne2 Consider adding importFrom("grDevices", "rgb") to your NAMESPACE file.

• checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘SingleCellExperiment’

• checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘BiocManager’ 'library' or 'require' call not declared from: ‘Matrix’

autonomics

• Version: 1.4.0
• GitHub: https://github.com/bhagwataditya/autonomics
• Source code: https://github.com/cran/autonomics
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 205

Run revdep_details(, "autonomics") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘using_autonomics.Rmd’ using rmarkdown Error: processing vignette 'using_autonomics.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘using_autonomics.Rmd’

  SUMMARY: processing the following file failed: ‘using_autonomics.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'normimpute' ‘ref’ ‘pos’

  Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

BANDITS

• Version: 1.12.0
• GitHub: https://github.com/SimoneTiberi/BANDITS
• Source code: https://github.com/cran/BANDITS
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 145

Run revdep_details(, "BANDITS") for more info

In both

• checking installed package size ... NOTE installed size is 9.8Mb sub-directories of 1Mb or more: extdata 1.3Mb libs 7.0Mb

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R.utils’ All declared Imports should be used.

• checking R code for possible problems ... NOTE infer_one_group: no visible binding for global variable ‘p’ plot_precision: no visible binding for global variable ‘x’ test_DTU: no visible binding for global variable ‘p’ test_DTU_multi_group: no visible binding for global variable ‘p’ Undefined global functions or variables: p x

bigsnpr

• Version: 1.11.4
• GitHub: https://github.com/privefl/bigsnpr
• Source code: https://github.com/cran/bigsnpr
• Date/Publication: 2022-10-21 16:05:07 UTC
• Number of recursive dependencies: 148

Run revdep_details(, "bigsnpr") for more info

In both

• checking installed package size ... NOTE installed size is 18.6Mb sub-directories of 1Mb or more: libs 17.3Mb

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘runonce’ All declared Imports should be used.

biscuiteer

• Version: 1.10.0
• GitHub: https://github.com/trichelab/biscuiteer
• Source code: https://github.com/cran/biscuiteer
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 216

Run revdep_details(, "biscuiteer") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘biscuiteer.Rmd’ using rmarkdown Error: processing vignette 'biscuiteer.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘biscuiteer.Rmd’

  SUMMARY: processing the following file failed: ‘biscuiteer.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking whether package ‘biscuiteer’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’ See ‘/c4/home/henrik/repositories/R.utils/revdep/checks/biscuiteer/new/biscuiteer.Rcheck/00install.out’ for details.

• checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: data 1.1Mb extdata 3.4Mb

• checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘QDNAseq:::expectedVariance’ See the note in ?`:::` about the use of this operator.

bsseq

• Version: 1.32.0
• GitHub: https://github.com/kasperdanielhansen/bsseq
• Source code: https://github.com/cran/bsseq
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 126

Run revdep_details(, "bsseq") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘bsseq.Rmd’ using rmarkdown Loading required package: BiocGenerics

  Attaching package: 'BiocGenerics'

  The following objects are masked from 'package:stats':

  IQR, mad, sd, var, xtabs
  

  ... Quitting from lines 29-31 (bsseq_analysis.Rmd) Error: processing vignette 'bsseq_analysis.Rmd' failed with diagnostics: there is no package called 'bsseqData' --- failed re-building ‘bsseq_analysis.Rmd’

  SUMMARY: processing the following file failed: ‘bsseq_analysis.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking package dependencies ... NOTE Package suggested but not available for checking: ‘bsseqData’

• checking installed package size ... NOTE installed size is 8.6Mb sub-directories of 1Mb or more: data 1.9Mb doc 1.9Mb libs 3.7Mb

• checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘DelayedArray:::get_verbose_block_processing’ ‘DelayedArray:::normarg_grid’ ‘GenomicRanges:::.extract_groups_from_GenomicRanges’ ‘GenomicRanges:::.get_circle_length’ ‘GenomicRanges:::extraColumnSlotNames’ ‘IRanges:::.shift_ranges_in_groups_to_first_circle’ ‘S4Vectors:::normarg_names’ ‘S4Vectors:::numeric2integer’ ‘S4Vectors:::sapply_isNULL’ ‘data.table:::funique’ See the note in ?`:::` about the use of this operator.

• checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘bsseqData’

casabourse

• Version: 2.0.0
• GitHub: https://github.com/NA/NA
• Source code: https://github.com/cran/casabourse
• Date/Publication: 2022-08-19 21:30:09 UTC
• Number of recursive dependencies: 48

Run revdep_details(, "casabourse") for more info

In both

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R.utils’ All declared Imports should be used.

CB2

• Version: 1.3.4
• GitHub: NA
• Source code: https://github.com/cran/CB2
• Date/Publication: 2020-07-24 09:42:24 UTC
• Number of recursive dependencies: 110

Run revdep_details(, "CB2") for more info

In both

• checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: data 1.5Mb extdata 1.1Mb libs 4.3Mb

cifti

• Version: 0.4.5
• GitHub: NA
• Source code: https://github.com/cran/cifti
• Date/Publication: 2018-02-01 23:25:24 UTC
• Number of recursive dependencies: 49

Run revdep_details(, "cifti") for more info

In both

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

civis

• Version: 3.0.0
• GitHub: https://github.com/civisanalytics/civis-r
• Source code: https://github.com/cran/civis
• Date/Publication: 2020-06-22 18:00:02 UTC
• Number of recursive dependencies: 88

Run revdep_details(, "civis") for more info

In both

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

cmdfun

• Version: 1.0.2
• GitHub: https://github.com/snystrom/cmdfun
• Source code: https://github.com/cran/cmdfun
• Date/Publication: 2020-10-10 09:30:03 UTC
• Number of recursive dependencies: 71

Run revdep_details(, "cmdfun") for more info

In both

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

cmsaf

• Version: 3.4.4
• GitHub: https://github.com/cmsaf/cmsaf-r-tools
• Source code: https://github.com/cran/cmsaf
• Date/Publication: 2022-08-15 14:50:10 UTC
• Number of recursive dependencies: 125

Run revdep_details(, "cmsaf") for more info

In both

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’ ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’ ‘rworldxtra’ ‘shinyFiles’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘sp’ ‘tcltk’ ‘xml2’ All declared Imports should be used.

CNEr

• Version: 1.32.0
• GitHub: https://github.com/ge11232002/CNEr
• Source code: https://github.com/cran/CNEr
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 177

Run revdep_details(, "CNEr") for more info

In both

• checking compiled code ... WARNING ``` File ‘CNEr/libs/CNEr.so’: Found ‘abort’, possibly from ‘abort’ (C) Object: ‘ucsc/errabort.o’ Found ‘exit’, possibly from ‘exit’ (C) Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’ Found ‘printf’, possibly from ‘printf’ (C) Objects: ‘ceScan.o’, ‘ucsc/pipeline.o’ Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) Object: ‘ucsc/pipeline.o’ Found ‘rand’, possibly from ‘rand’ (C) ... ‘ucsc/verbose.o’, ‘ucsc/os.o’ Found ‘stdout’, possibly from ‘stdout’ (C) Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/verbose.o’, ‘ucsc/os.o’

  Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs.

  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

• checking installed package size ... NOTE installed size is 20.3Mb sub-directories of 1Mb or more: doc 1.8Mb extdata 15.9Mb libs 1.3Mb

• checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’ See the note in ?`:::` about the use of this operator.

CNVgears

• Version: 1.4.0
• GitHub: https://github.com/SinomeM/CNVgears
• Source code: https://github.com/cran/CNVgears
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 198

Run revdep_details(, "CNVgears") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘CNVgears.Rmd’ using rmarkdown Error: processing vignette 'CNVgears.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘CNVgears.Rmd’

  SUMMARY: processing the following file failed: ‘CNVgears.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: data 1.4Mb extdata 3.6Mb

• checking R code for possible problems ... NOTE CNVresults_to_GRanges: no visible global function definition for ‘.’ CNVresults_to_GRanges: no visible binding for global variable ‘sample_ID’ CNVresults_to_GRanges: no visible binding for global variable ‘GT’ CNVresults_to_GRanges: no visible binding for global variable ‘meth_ID’ CNVresults_to_GRangesList: no visible binding for global variable ‘GRL’ DT_uniform_internal: no visible binding for global variable ‘chr’ DT_uniform_internal: no visible binding for global variable ‘start’ DT_uniform_internal: no visible binding for global variable ‘end’ DT_uniform_internal: no visible binding for global variable ‘CN’ ... inheritance ix last_P len locus locus_end locus_start log2R m_pval mean_len meth_ID mmmethod n_cnvs outer_end outer_start p.adjust p_pval pdf pos r_ID reorder role sample_ID sd seg_ID sex start tail used wilcox.test Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("stats", "end", "p.adjust", "reorder", "sd", "start", "wilcox.test") importFrom("utils", "head", "tail") to your NAMESPACE file.

cometr

• Version: 0.2.0
• GitHub: https://github.com/comet-ml/cometr
• Source code: https://github.com/cran/cometr
• Date/Publication: 2020-08-13 17:40:03 UTC
• Number of recursive dependencies: 46

Run revdep_details(, "cometr") for more info

In both

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R6’ All declared Imports should be used.

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

COTAN

• Version: 1.0.0
• GitHub: https://github.com/seriph78/COTAN
• Source code: https://github.com/cran/COTAN
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 195

Run revdep_details(, "COTAN") for more info

In both

• checking examples ... ERROR ``` Running examples in ‘COTAN-Ex.R’ failed The error most likely occurred in:

  Name: automatic.COTAN.object.creation

  Title: automatic.COTAN.object.creation

  Aliases: automatic.COTAN.object.creation

  automatic.COTAN.object.creation,data.frame-method

  ** Examples

  ... + cond = "test") [1] "Initializing S4 object" [1] "Condition test" [1] "n cells 815" [1] "Start estimation mu with linear method" [1] 2001 815 Error in py_run_file_impl(file, local, convert) : ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /c4/home/henrik/.cache/R/basilisk/1.8.1/COTAN/1.0.0/my_env_cotan/lib/python3.7/site-packages/pandas/_libs/window/aggregations.cpython-37m-x86_64-linux-gnu.so) Calls: automatic.COTAN.object.creation ... -> -> py_run_file -> py_run_file_impl Execution halted ```

• checking tests ... `` Running ‘spelling.R’ Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6 < NULL --- > All Done! Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: Error inpy_run_file_impl(file, local, convert): ImportError: /lib64/libstdc++.so.6: versionGLIBCXX_3.4.21' not found (required by /c4/home/henrik/.cache/R/basilisk/1.8.1/COTAN/1.0.0/my_env_cotan/lib/python3.7/site-packages/pandas/_libs/window/aggregations.cpython-37m-x86_64-linux-gnu.so) ... ── Error ('test-my-test.R:120'): 5.get_pval_test ─────────────────────────────── Error in gzfile(file, "rb"): cannot open the connection Backtrace: ▆

  1. └─base::readRDS(file.path(tm, "temp.RDS")) at test-my-test.R:120:4
  2. └─base::gzfile(file, "rb")

  [ FAIL 5 | WARN 3 | SKIP 0 | PASS 6 ] Error: Test failures Execution halted ```

• checking re-building of vignette outputs ... ERROR `` Error(s) in re-building vignettes: ... --- re-building ‘Guided_tutorial.Rmd’ using rmarkdown Quitting from lines 131-136 (Guided_tutorial.Rmd) Error: processing vignette 'Guided_tutorial.Rmd' failed with diagnostics: ImportError: /lib64/libstdc++.so.6: versionGLIBCXX_3.4.21' not found (required by /c4/home/henrik/.cache/R/basilisk/1.8.1/COTAN/1.0.0/my_env_cotan/lib/python3.7/site-packages/pandas/_libs/window/aggregations.cpython-37m-x86_64-linux-gnu.so)

  --- failed re-building ‘Guided_tutorial.Rmd’

  SUMMARY: processing the following file failed: ‘Guided_tutorial.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

countyfloods

• Version: 0.1.0
• GitHub: NA
• Source code: https://github.com/cran/countyfloods
• Date/Publication: 2017-10-26 03:22:55 UTC
• Number of recursive dependencies: 104

Run revdep_details(, "countyfloods") for more info

In both

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘maps’ All declared Imports should be used.

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

cRegulome

• Version: 0.3.2
• GitHub: https://github.com/ropensci/cRegulome
• Source code: https://github.com/cran/cRegulome
• Date/Publication: 2020-05-08 13:20:09 UTC
• Number of recursive dependencies: 158

Run revdep_details(, "cRegulome") for more info

In both

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

cTRAP

• Version: 1.14.1
• GitHub: https://github.com/nuno-agostinho/cTRAP
• Source code: https://github.com/cran/cTRAP
• Date/Publication: 2022-07-17
• Number of recursive dependencies: 171

Run revdep_details(, "cTRAP") for more info

In both

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: .devcontainer These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

• checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: data 4.3Mb doc 1.9Mb

• checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘cTRAP/R/shinyInterface_session.R’: assignInNamespace("dataTablesFilter", dt_mod, "DT")

• checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

ddPCRclust

• Version: 1.16.0
• GitHub: https://github.com/bgbrink/ddPCRclust
• Source code: https://github.com/cran/ddPCRclust
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 160

Run revdep_details(, "ddPCRclust") for more info

In both

• checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘ddPCRclust.Rnw’ using Sweave Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’ double positive detection failed. Switching the middle two double populations.

  Starting the flow Peaks analysis...

  Task A: compute kmeans...
  

  ... l.189 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘ddPCRclust.Rnw’

  SUMMARY: processing the following file failed: ‘ddPCRclust.Rnw’

  Error: Vignette re-building failed. Execution halted ```

DeepBlueR

• Version: 1.22.0
• GitHub: NA
• Source code: https://github.com/cran/DeepBlueR
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 159

Run revdep_details(, "DeepBlueR") for more info

In both

• checking Rd files ... NOTE prepare_Rd: deepblue_enrich_regions_fast.Rd:35-38: Dropping empty section \examples

DEGraph

• Version: 1.48.0
• GitHub: NA
• Source code: https://github.com/cran/DEGraph
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 79

Run revdep_details(, "DEGraph") for more info

In both

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

• checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘graph’ ‘KEGGgraph’ ‘lattice’ ‘RBGL’ ‘rrcov’ ‘Rgraphviz’ ‘NCIgraph’ A package should be listed in only one of these fields.

• checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘R.utils’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘graph:::getIndices’ See the note in ?`:::` about the use of this operator.

detrendr

• Version: 0.6.14
• GitHub: https://github.com/rorynolan/detrendr
• Source code: https://github.com/cran/detrendr
• Date/Publication: 2021-05-16 05:00:05 UTC
• Number of recursive dependencies: 115

Run revdep_details(, "detrendr") for more info

In both

• checking installed package size ... NOTE installed size is 10.0Mb sub-directories of 1Mb or more: libs 8.9Mb

• checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

DEWSeq

• Version: 1.10.0
• GitHub: https://github.com/EMBL-Hentze-group/DEWSeq
• Source code: https://github.com/cran/DEWSeq
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 123

Run revdep_details(, "DEWSeq") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘DEWSeq.Rmd’ using rmarkdown Loading required package: DEWSeq Loading required package: R.utils Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help. R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.

  Attaching package: 'R.oo' ... Quitting from lines 506-507 (DEWSeq.Rmd) Error: processing vignette 'DEWSeq.Rmd' failed with diagnostics: could not find function "read_tsv" --- failed re-building ‘DEWSeq.Rmd’

  SUMMARY: processing the following file failed: ‘DEWSeq.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘R.utils’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: ‘DESeq2:::checkContrast’ ‘DESeq2:::cleanContrast’ ‘DESeq2:::getCoef’ ‘DESeq2:::getCoefSE’ ‘DESeq2:::getNworkers’ ‘DESeq2:::getPvalue’ ‘DESeq2:::getStat’ ‘DESeq2:::lastCoefName’ ‘DESeq2:::makeWaldTest’ ‘DESeq2:::mleContrast’ See the note in ?`:::` about the use of this operator.

• checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘dplyr’ 'library' or 'require' call not declared from: ‘tidyverse’

DropletUtils

• Version: 1.16.0
• GitHub: NA
• Source code: https://github.com/cran/DropletUtils
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 135

Run revdep_details(, "DropletUtils") for more info

In both

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

• checking installed package size ... NOTE installed size is 26.1Mb sub-directories of 1Mb or more: libs 24.8Mb

• checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

Eagle

• Version: 2.5
• GitHub: NA
• Source code: https://github.com/cran/Eagle
• Date/Publication: 2021-11-30 05:30:02 UTC
• Number of recursive dependencies: 81

Run revdep_details(, "Eagle") for more info

In both

• checking installed package size ... NOTE installed size is 20.2Mb sub-directories of 1Mb or more: libs 18.8Mb shiny_app 1.0Mb

easyDifferentialGeneCoexpression

• Version: 1.0
• GitHub: https://github.com/davidechicco/easyDifferentialGeneCoexpression
• Source code: https://github.com/cran/easyDifferentialGeneCoexpression
• Date/Publication: 2022-02-16 20:20:07 UTC
• Number of recursive dependencies: 148

Run revdep_details(, "easyDifferentialGeneCoexpression") for more info

In both

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R.utils’ ‘stringi’ All declared Imports should be used.

eegc

• Version: 1.22.0
• GitHub: NA
• Source code: https://github.com/cran/eegc
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 152

Run revdep_details(, "eegc") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘eegc.Rnw’ using knitr Quitting from lines 27-28 (eegc.Rnw) Error: processing vignette 'eegc.Rnw' failed with diagnostics: there is no package called 'BiocStyle' --- failed re-building ‘eegc.Rnw’

  SUMMARY: processing the following file failed: ‘eegc.Rnw’

  Error: Vignette re-building failed. Execution halted ```

• checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'barplotEnrich.Rd': ‘[DOSE]{barplot.enrichResult}’

  See section 'Cross-references' in the 'Writing R Extensions' manual. ```

• checking LazyData ... WARNING LazyData DB of 10.5 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions'

• checking installed package size ... NOTE installed size is 11.5Mb sub-directories of 1Mb or more: data 10.5Mb

• checking R code for possible problems ... NOTE categorizeGene : <anonymous>: no visible global function definition for ‘quantile’ densityPlot: no visible binding for global variable ‘density’ densityPlot: no visible global function definition for ‘lines’ densityPlot: no visible global function definition for ‘axis’ densityPlot: no visible global function definition for ‘adjustcolor’ densityPlot: no visible global function definition for ‘legend’ densityPlot : <anonymous>: no visible global function definition for ‘quantile’ densityPlot: no visible global function definition for ‘text’ ... legend lines lm model.matrix p.adjust par phyper points quantile results text title treat Consider adding importFrom("grDevices", "adjustcolor", "colorRampPalette", "dev.copy2pdf") importFrom("graphics", "abline", "axis", "legend", "lines", "par", "points", "text", "title") importFrom("stats", "density", "lm", "model.matrix", "p.adjust", "phyper", "quantile") to your NAMESPACE file.

• checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘BiocStyle’

ELMER

• Version: 2.20.0
• GitHub: NA
• Source code: https://github.com/cran/ELMER
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 228

Run revdep_details(, "ELMER") for more info

In both

• checking dependencies in R code ... WARNING Missing or unexported object: 'TCGAbiolinks::GDCquery_Maf'

• checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'render_report': render_report Code: function(title = "Report", mae.file, group.col, group1, group2, direction, dir.out, genome = "hg38", mode = "supervised", minSubgroupFrac = 0.2, minMetdiff = 0.3, metfdr = 0.01, permu = 10000, rawpval = 0.01, pe = 0.01, nprobes = 10, lower.OR = 1.1, out_file = file.path(getwd(), "report.html"), funcivar = FALSE) Docs: function(title = "Report", mae.file, group.col, group1, group2, direction, dir.out, genome = "hg38", mode = "supervised", minSubgroupFrac = "20%", minMetdiff = "0.3", metfdr = "0.01", permu = "10000", rawpval = "0.01", pe = "0.01", nprobes = "10", lower.OR = "1.1", out_file = file.path(getwd(), "report.html"), funcivar = FALSE) Mismatches in argument default values: Name: 'minSubgroupFrac' Code: 0.2 Docs: "20%"

• checking installed package size ... NOTE installed size is 75.2Mb sub-directories of 1Mb or more: doc 74.7Mb

• checking R code for possible problems ... NOTE TCGA.pipe: warning in render_report(genome = genome, mode = mode, title = paste0(disease, " report"), minSubgroupFrac = ifelse(mode == "supervised", 1, 0.2), mae = mae.path, direction = direction, group.col = group.col, group1 = group1, group2 = group2, dir.out = results.path, out_file = file.path(results.path, paste0(disease, "_report.html"))): partial argument match of 'mae' to 'mae.file' Stat.nonpara: no visible global function definition for 'head' Stat.nonpara: no visible global function definition for 'tail' Stat.nonpara.permu: no visible global function definition for 'head' Stat.nonpara.permu: no visible global function definition for 'tail' ... 'DistanceTSS' get.top.tf.by.pval: no visible global function definition for 'head' getRegionNearGenes : f: no visible binding for global variable 'Side' getRegionNearGenes: no visible binding for global variable 'ID' getTFtargets: no visible binding for global variable 'TF' Undefined global functions or variables: DistanceTSS Hugo_Symbol ID Side TF head tail Consider adding importFrom("utils", "head", "tail") to your NAMESPACE file.

enrichTF

• Version: 1.12.0
• GitHub: https://github.com/wzthu/enrichTF
• Source code: https://github.com/cran/enrichTF
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 209

Run revdep_details(, "enrichTF") for more info

In both

• checking examples ... ERROR ``` Running examples in ‘enrichTF-Ex.R’ failed The error most likely occurred in:

  Name: GenBackground

  Title: Generate background regions and reset the size of foreground

  regions

  Aliases: GenBackground enrichGenBackground,Step-method

  enrichGenBackground genBackground

  ** Examples

  setGenome("testgenome") #Use "hg19","hg38",etc. for your application Configure bsgenome ... Error in get_data_annotation_contrib_url(type) : Install 'BiocManager' from CRAN to get 'BioCann' contrib.url Calls: setGenome ... checkAndInstallBSgenome -> -> get_data_annotation_contrib_url Execution halted ```

• checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(enrichTF) Loading required package: pipeFrame

  test_check("enrichTF") ... 4. └─enrichTF (local) cai() 5. └─pipeFrame::runWithFinishCheck(...) 6. └─enrichTF (local) func(NULL) 7. └─pipeFrame::checkAndInstallBSgenome(refFilePath, genome) 8. └─BSgenome::available.genomes() 9. └─BSgenome:::get_data_annotation_contrib_url(type)

  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted ```

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘enrichTF.Rmd’ using rmarkdown Loading required package: pipeFrame

  Quitting from lines 58-62 (enrichTF.Rmd) Error: processing vignette 'enrichTF.Rmd' failed with diagnostics: Install 'BiocManager' from CRAN to get 'BioCann' contrib.url --- failed re-building ‘enrichTF.Rmd’

  SUMMARY: processing the following file failed: ‘enrichTF.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking R code for possible problems ... NOTE processing,TissueOpennessConserve: no visible binding for global variable ‘X2’ Undefined global functions or variables: X2

EpiNow2

• Version: 1.3.2
• GitHub: https://github.com/epiforecasts/EpiNow2
• Source code: https://github.com/cran/EpiNow2
• Date/Publication: 2020-12-14 09:00:15 UTC
• Number of recursive dependencies: 159

Run revdep_details(, "EpiNow2") for more info

In both

• checking package dependencies ... NOTE Package suggested but not available for checking: ‘EpiSoon’

• checking installed package size ... NOTE installed size is 225.9Mb sub-directories of 1Mb or more: libs 224.3Mb

esATAC

• Version: 1.18.0
• GitHub: https://github.com/wzthu/esATAC
• Source code: https://github.com/cran/esATAC
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 228

Run revdep_details(, "esATAC") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘esATAC-Introduction.Rmd’ using rmarkdown Error: processing vignette 'esATAC-Introduction.Rmd' failed with diagnostics: there is no package called ‘prettydoc’ --- failed re-building ‘esATAC-Introduction.Rmd’

  SUMMARY: processing the following file failed: ‘esATAC-Introduction.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'PeakCallingMACS2' ‘genomeSize’ ‘pvalueThreshold’ Documented arguments not in \usage in documentation object 'PeakCallingMACS2': ‘threshold’

  Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

• checking installed package size ... NOTE installed size is 14.3Mb sub-directories of 1Mb or more: doc 3.3Mb extdata 5.1Mb libs 4.9Mb

• checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘ShortRead:::.ShortReadQQA’ ‘ShortRead:::.qa_adapterContamination’ See the note in ?`:::` about the use of this operator.

• checking R code for possible problems ... NOTE atacPipe2: no visible global function definition for ‘getObjsInPipe’ atacPipe2: no visible binding for global variable ‘case.peak’ atacPipe2: no visible binding for global variable ‘ctrl.peak’ atacPipe2: no visible binding for global variable ‘pwm’ atacPipe2: no visible binding for global variable ‘bed.case’ atacPipe2: no visible binding for global variable ‘bed.ctrl’ atacPipe2: no visible binding for global variable ‘caselist’ atacPipe2: no visible binding for global variable ‘ctrllist’ atacPipe2: no visible global function definition for ‘.obtainConfigure’ atacPipe2: no visible binding for global variable ‘param.tmp’ ... atacPipe2: no visible binding for global variable ‘esATAC_report’ atacPipe2: no visible global function definition for ‘getReportVal’ atacPipe2: no visible binding for global variable ‘esATAC_result’ processing,BamToBed : <anonymous>: no visible global function definition for ‘readGAlignments’ processing,BedToBigWig: no visible binding for global variable ‘score’ Undefined global functions or variables: .obtainConfigure bed.case bed.ctrl case.peak caselist ctrl.peak ctrllist esATAC_report esATAC_result getObjsInPipe getReportVal param.tmp pwm readGAlignments score

eudysbiome

• Version: 1.26.0
• GitHub: NA
• Source code: https://github.com/cran/eudysbiome
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 27

Run revdep_details(, "eudysbiome") for more info

In both

• checking R code for possible problems ... NOTE Cartesian: no visible global function definition for ‘adjustcolor’ Cartesian: no visible global function definition for ‘colors’ Cartesian: no visible global function definition for ‘dev.hold’ Cartesian: no visible global function definition for ‘dev.flush’ Cartesian: no visible global function definition for ‘points’ Cartesian: no visible global function definition for ‘abline’ Cartesian: no visible global function definition for ‘axis’ Cartesian: no visible global function definition for ‘text’ Cartesian: no visible global function definition for ‘par’ Cartesian: no visible global function definition for ‘mtext’ ... read.table rect text title unzip Consider adding importFrom("grDevices", "adjustcolor", "colors", "dev.flush", "dev.hold") importFrom("graphics", "abline", "axis", "mtext", "par", "points", "rect", "text", "title") importFrom("stats", "chisq.test") importFrom("utils", "combn", "data", "download.file", "read.table", "unzip") to your NAMESPACE file.

ezknitr

• Version: 0.6
• GitHub: https://github.com/ropenscilabs/ezknitr
• Source code: https://github.com/cran/ezknitr
• Date/Publication: 2016-09-16 07:13:44
• Number of recursive dependencies: 53

Run revdep_details(, "ezknitr") for more info

In both

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

fastreeR

• Version: 1.0.0
• GitHub: https://github.com/gkanogiannis/fastreeR
• Source code: https://github.com/cran/fastreeR
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 86

Run revdep_details(, "fastreeR") for more info

In both

• R CMD check timed out

FCPS

• Version: 1.3.1
• GitHub: https://github.com/Mthrun/FCPS
• Source code: https://github.com/cran/FCPS
• Date/Publication: 2022-05-20 16:40:05 UTC
• Number of recursive dependencies: 267

Run revdep_details(, "FCPS") for more info

In both

• checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: data 2.3Mb doc 3.9Mb

FGNet

• Version: 3.30.0
• GitHub: NA
• Source code: https://github.com/cran/FGNet
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 79

Run revdep_details(, "FGNet") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘FGNet.Rmd’ using rmarkdown Quitting from lines 89-90 (FGNet.Rmd) Error: processing vignette 'FGNet.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘FGNet.Rmd’

  SUMMARY: processing the following file failed: ‘FGNet.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘RGtk2’

fitteR

• Version: 0.2.0
• GitHub: NA
• Source code: https://github.com/cran/fitteR
• Date/Publication: 2022-02-22 12:00:02 UTC
• Number of recursive dependencies: 211

Run revdep_details(, "fitteR") for more info

In both

• checking package dependencies ... NOTE Package suggested but not available for checking: ‘reliaR’

FRASER

• Version: 1.8.1
• GitHub: https://github.com/gagneurlab/FRASER
• Source code: https://github.com/cran/FRASER
• Date/Publication: 2022-06-30
• Number of recursive dependencies: 188

Run revdep_details(, "FRASER") for more info

In both

• checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘FRASER.Rnw’ using knitr Mon Oct 24 01:10:41 2022: Start counting the split reads ... Mon Oct 24 01:10:42 2022: Count split reads for sample: sample1 Mon Oct 24 01:10:45 2022: Count split reads for sample: sample2 Mon Oct 24 01:10:46 2022: Count split reads for sample: sample3 Mon Oct 24 01:10:52 2022 : count ranges need to be merged ... Mon Oct 24 01:10:52 2022: Create splice site indices ... Mon Oct 24 01:10:52 2022: Writing split counts to folder: FRASER_output/savedObjects/Data_Analysis/splitCounts Mon Oct 24 01:10:56 2022: Identifying introns with read count <= 20 in all samples... ... l.189 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘FRASER.Rnw’

  SUMMARY: processing the following file failed: ‘FRASER.Rnw’

  Error: Vignette re-building failed. Execution halted ```

• checking installed package size ... NOTE installed size is 9.6Mb sub-directories of 1Mb or more: R 1.3Mb doc 1.6Mb libs 6.0Mb

• checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’ See the note in ?`:::` about the use of this operator.

GCSscore

• Version: 1.10.0
• GitHub: NA
• Source code: https://github.com/cran/GCSscore
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 134

Run revdep_details(, "GCSscore") for more info

In both

• checking running R code from vignettes ... ``` ‘GCSscore.Rnw’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘GCSscore.Rnw’ ... This package will only be generated once for each chip-type Or if probeFile version for the chip-type needs to be updated writing intermediary .probe_tab file to temporary directory Importing the data. Warning in packageDescription(thispkg) : no package 'AnnotationForge' was found

  When sourcing ‘GCSscore.R’: Error: $ operator is invalid for atomic vectors Execution halted ```

• checking installed package size ... NOTE installed size is 11.9Mb sub-directories of 1Mb or more: extdata 11.6Mb

• checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘GCSscore.Rnw’ using Sweave GCSscore supports the selected chip-type: Clariom_S_Mouse Bioconductor platform design (.pd) package already installed for: Clariom_S_Mouse GCS-score analysis initiated for chip-type: Clariom_S_Mouse GCS-score 'probeFile' package needs to be installed for chip-type: Clariom_S_Mouse typeFilter set to (0) by default for best .CEL file scaling and normalization statistics all probe_id types (including control probe_ids and bgp probe_ids) will be for GCS-score calculation. it is generally recommended to leave the typeFilter option set to (0)

geneExpressionFromGEO

• Version: 0.9
• GitHub: https://github.com/davidechicco/geneExpressionFromGEO
• Source code: https://github.com/cran/geneExpressionFromGEO
• Date/Publication: 2021-12-16 08:40:02 UTC
• Number of recursive dependencies: 88

Run revdep_details(, "geneExpressionFromGEO") for more info

In both

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘BiocManager’ ‘R.utils’ ‘markdown’ All declared Imports should be used.

GEOquery

• Version: 2.64.2
• GitHub: https://github.com/seandavi/GEOquery
• Source code: https://github.com/cran/GEOquery
• Date/Publication: 2022-05-15
• Number of recursive dependencies: 81

Run revdep_details(, "GEOquery") for more info

In both

• checking installed package size ... NOTE installed size is 13.8Mb sub-directories of 1Mb or more: extdata 12.8Mb

• checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT

• checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.

• checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘GEOquery’ for: ‘show’

  A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

  Probably some imports need to be declared in the NAMESPACE file. ```

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R.utils’ All declared Imports should be used. Package in Depends field not imported from: ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

• checking R code for possible problems ... NOTE ``` File ‘GEOquery/R/zzz.R’: .onLoad calls: packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')") packageStartupMessage("Setting options('GEOquery.inmemory.gpl'=FALSE)")

  See section ‘Good practice’ in '?.onAttach'. ```

gifti

• Version: 0.8.0
• GitHub: https://github.com/muschellij2/gifti
• Source code: https://github.com/cran/gifti
• Date/Publication: 2020-11-11 22:40:02 UTC
• Number of recursive dependencies: 63

Run revdep_details(, "gifti") for more info

In both

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

HiCBricks

• Version: 1.14.0
• GitHub: NA
• Source code: https://github.com/cran/HiCBricks
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 96

Run revdep_details(, "HiCBricks") for more info

In both

• checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: doc 4.4Mb extdata 2.2Mb

HiCDCPlus

• Version: 1.4.2
• GitHub: NA
• Source code: https://github.com/cran/HiCDCPlus
• Date/Publication: 2022-06-07
• Number of recursive dependencies: 168

Run revdep_details(, "HiCDCPlus") for more info

In both

• checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: extdata 3.3Mb libs 2.0Mb

hoardeR

• Version: 0.9.4-2
• GitHub: NA
• Source code: https://github.com/cran/hoardeR
• Date/Publication: 2019-02-12 08:23:21 UTC
• Number of recursive dependencies: 73

Run revdep_details(, "hoardeR") for more info

In both

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘knitr’ ‘rmarkdown’ All declared Imports should be used.

HyPhy

• Version: 1.0
• GitHub: NA
• Source code: https://github.com/cran/HyPhy
• Date/Publication: 2012-07-30 04:09:01
• Number of recursive dependencies: 7

Run revdep_details(, "HyPhy") for more info

In both

• checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘R.utils’ ‘ape’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

ISAnalytics

• Version: 1.6.2
• GitHub: https://github.com/calabrialab/ISAnalytics
• Source code: https://github.com/cran/ISAnalytics
• Date/Publication: 2022-05-24
• Number of recursive dependencies: 159

Run revdep_details(, "ISAnalytics") for more info

In both

• checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: data 1.4Mb doc 4.3Mb

• checking R code for possible problems ... NOTE .sh_row_permut: no visible global function definition for ‘.’ .sharing_multdf_mult_key: no visible binding for global variable ‘.’ .sharing_multdf_single_key: no visible binding for global variable ‘.’ .sharing_singledf_mult_key: no visible binding for global variable ‘.’ .sharing_singledf_single_key: no visible binding for global variable ‘.’ cumulative_is: no visible binding for global variable ‘is’ gene_frequency_fisher: no visible binding for global variable ‘.’ sharing_heatmap : plot_rel_heat: no visible binding for global variable ‘..fill..’ Undefined global functions or variables: . ..fill.. is Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

joinXL

• Version: 1.0.1
• GitHub: https://github.com/yvonneglanville/joinXL
• Source code: https://github.com/cran/joinXL
• Date/Publication: 2016-09-19 01:45:37
• Number of recursive dependencies: 53

Run revdep_details(, "joinXL") for more info

In both

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

jsTreeR

• Version: 2.2.0
• GitHub: https://github.com/stla/jsTreeR
• Source code: https://github.com/cran/jsTreeR
• Date/Publication: 2022-10-21 08:55:07 UTC
• Number of recursive dependencies: 39

Run revdep_details(, "jsTreeR") for more info

In both

• checking data for non-ASCII characters ... NOTE Note: found 17 marked UTF-8 strings

KnowSeq

• Version: 1.10.2
• GitHub: NA
• Source code: https://github.com/cran/KnowSeq
• Date/Publication: 2022-07-03
• Number of recursive dependencies: 162

Run revdep_details(, "KnowSeq") for more info

In both

• checking installed package size ... NOTE installed size is 12.9Mb sub-directories of 1Mb or more: doc 5.8Mb extdata 6.9Mb

• checking R code for possible problems ... NOTE DEGsExtraction: warning in topTable(fit, number = number, coef = 2, sort.by = "logFC", p.value = pvalue, adjust = "fdr", lfc = lfc): partial argument match of 'adjust' to 'adjust.method' RNAseqQA : outlierBarPlot: no visible binding for global variable ‘x’ RNAseqQA : outlierBarPlot: no visible binding for global variable ‘y’ RNAseqQA: no visible binding for global variable ‘Var1’ RNAseqQA: no visible binding for global variable ‘Var2’ RNAseqQA: no visible binding for global variable ‘value’ RNAseqQA: no visible binding for global variable ‘Expression’ RNAseqQA: no visible binding for global variable ‘Samples’ dataPlot: no visible binding for global variable ‘Var1’ dataPlot: no visible binding for global variable ‘Var2’ dataPlot: no visible binding for global variable ‘value’ dataPlot: no visible binding for global variable ‘Classes’ dataPlot: no visible binding for global variable ‘Value’ knn_trn: no visible global function definition for ‘knn.cv’ knowseqReport: no visible binding for global variable ‘target’ Undefined global functions or variables: Classes Expression Samples Value Var1 Var2 knn.cv target value x y

latrend

• Version: 1.4.2
• GitHub: https://github.com/philips-software/latrend
• Source code: https://github.com/cran/latrend
• Date/Publication: 2022-08-15 11:40:05 UTC
• Number of recursive dependencies: 238

Run revdep_details(, "latrend") for more info

In both

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rmarkdown’ All declared Imports should be used.

logger

• Version: 0.2.2
• GitHub: https://github.com/daroczig/logger
• Source code: https://github.com/cran/logger
• Date/Publication: 2021-10-19 05:30:08 UTC
• Number of recursive dependencies: 135

Run revdep_details(, "logger") for more info

In both

• checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘botor’

  Packages which this enhances but not available for checking: 'logging', 'futile.logger', 'log4r' ```

macrocol

• Version: 0.1.0
• GitHub: NA
• Source code: https://github.com/cran/macrocol
• Date/Publication: 2022-09-09 08:13:01 UTC
• Number of recursive dependencies: 37

Run revdep_details(, "macrocol") for more info

In both

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R.utils’ All declared Imports should be used.

MACSQuantifyR

• Version: 1.10.0
• GitHub: NA
• Source code: https://github.com/cran/MACSQuantifyR
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 95

Run revdep_details(, "MACSQuantifyR") for more info

In both

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: revdep/.cache.rds These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

maftools

• Version: 2.12.0
• GitHub: https://github.com/PoisonAlien/maftools
• Source code: https://github.com/cran/maftools
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 119

Run revdep_details(, "maftools") for more info

In both

• checking installed package size ... NOTE installed size is 18.1Mb sub-directories of 1Mb or more: doc 8.7Mb extdata 6.0Mb libs 2.5Mb

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rhtslib’ All declared Imports should be used.

• checking R code for possible problems ... NOTE .dnaCopy_plotter: no visible binding for global variable ‘contig’ .dnaCopy_plotter: no visible binding for global variable ‘Chromosome’ .dnaCopy_plotter: no visible global function definition for ‘par’ .dnaCopy_plotter: no visible global function definition for ‘abline’ .dnaCopy_plotter: no visible global function definition for ‘segments’ .dnaCopy_plotter: no visible global function definition for ‘axis’ .mafSetKeys: no visible binding for global variable ‘Chromosome’ .mafSetKeys: no visible binding for global variable ‘Start_Position’ .mafSetKeys: no visible binding for global variable ‘End_Position’ OncogenicPathways: no visible binding for global variable ... "stripchart", "symbols", "text", "title") importFrom("stats", "C", "complete.cases", "cophenetic", "cor.test", "dbinom", "density", "fisher.test", "glm", "kmeans", "median", "na.omit", "p.adjust", "pairwise.t.test", "pairwise.table", "pchisq", "pnorm", "poisson", "poisson.test", "qf", "qnorm", "runif", "sd", "start", "t.test", "wilcox.test") importFrom("utils", "browseURL", "combn", "download.file", "read.csv", "setTxtProgressBar", "txtProgressBar", "write.table") to your NAMESPACE file.

• checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

• checking compiled code ... NOTE ``` File ‘maftools/libs/maftools.so’: Found ‘stderr’, possibly from ‘stderr’ (C) Object: ‘snpcounts.o’ Found ‘stdout’, possibly from ‘stdout’ (C) Object: ‘snpcounts.o’

  Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs.

  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

metaboliteIDmapping

• Version: 1.0.0
• GitHub: https://github.com/yigbt/metaboliteIDmapping
• Source code: https://github.com/cran/metaboliteIDmapping
• Number of recursive dependencies: 107

Run revdep_details(, "metaboliteIDmapping") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘metaboliteIDmapping.Rmd’ using rmarkdown Error: processing vignette 'metaboliteIDmapping.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘metaboliteIDmapping.Rmd’

  SUMMARY: processing the following file failed: ‘metaboliteIDmapping.Rmd’

  Error: Vignette re-building failed. Execution halted ```

MetaDBparse

• Version: 2.0.0
• GitHub: NA
• Source code: https://github.com/cran/MetaDBparse
• Date/Publication: 2021-05-03 14:00:11 UTC
• Number of recursive dependencies: 148

Run revdep_details(, "MetaDBparse") for more info

In both

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘pacman’ All declared Imports should be used.

MethReg

• Version: 1.6.0
• GitHub: https://github.com/TransBioInfoLab/MethReg
• Source code: https://github.com/cran/MethReg
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 221

Run revdep_details(, "MethReg") for more info

In both

• checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'methReg_analysis' ‘tf.dnam.classifier.pval.threshold’

  Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

• checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: R 1.6Mb doc 2.5Mb

• checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘TCGAbiolinks’

methylKit

• Version: 1.22.0
• GitHub: NA
• Source code: https://github.com/cran/methylKit
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 132

Run revdep_details(, "methylKit") for more info

In both

• checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'methylRawList-class' ‘...’ ‘treatment’

  Undocumented arguments in documentation object 'methylRawListDB-class' ‘...’ ‘treatment’

  Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

• checking installed package size ... NOTE installed size is 9.1Mb sub-directories of 1Mb or more: R 1.4Mb doc 1.4Mb libs 4.9Mb

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘KernSmooth’ All declared Imports should be used.

• checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

mirTarRnaSeq

• Version: 1.4.0
• GitHub: NA
• Source code: https://github.com/cran/mirTarRnaSeq
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 229

Run revdep_details(, "mirTarRnaSeq") for more info

In both

• checking examples ... ERROR ``` Running examples in ‘mirTarRnaSeq-Ex.R’ failed The error most likely occurred in:

  Name: mirRnaHeatmap

  Title: mirRnaHeatmap pheatmap for miRTarRNASeq miRNA and mRNA

  correlation

  Aliases: mirRnaHeatmap

  Keywords: color, correlation heatmap, pheatmap, plot,correlation_plot

  ** Examples

  x <- mirRnaHeatmap(corr_0) Error in loadNamespace(x) : there is no package called ‘viridis’ Calls: mirRnaHeatmap ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ```

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘mirTarRnaSeq.Rmd’ using rmarkdown Quitting from lines 17-36 (mirTarRnaSeq.Rmd) Error: processing vignette 'mirTarRnaSeq.Rmd' failed with diagnostics: there is no package called 'viridis' --- failed re-building ‘mirTarRnaSeq.Rmd’

  SUMMARY: processing the following file failed: ‘mirTarRnaSeq.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: data 3.6Mb

• checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘ggplot2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

• checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘tidyr’ ‘viridis’

mistyR

• Version: 1.4.0
• GitHub: https://github.com/saezlab/mistyR
• Source code: https://github.com/cran/mistyR
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 137

Run revdep_details(, "mistyR") for more info

In both

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘utils’ All declared Imports should be used.

msgbsR

• Version: 1.20.0
• GitHub: NA
• Source code: https://github.com/cran/msgbsR
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 167

Run revdep_details(, "msgbsR") for more info

In both

• checking installed package size ... NOTE installed size is 15.6Mb sub-directories of 1Mb or more: extdata 15.2Mb

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'utils' All declared Imports should be used.

muscData

• Version: 1.10.0
• GitHub: https://github.com/HelenaLC/muscData
• Source code: https://github.com/cran/muscData
• Date/Publication: 2022-04-28
• Number of recursive dependencies: 269

Run revdep_details(, "muscData") for more info

In both

• checking for missing documentation entries ... WARNING Undocumented code objects: ‘Crowell19_4vs4’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

• checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘SingleCellExperiment’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

nc

• Version: 2020.8.6
• GitHub: https://github.com/tdhock/nc
• Source code: https://github.com/cran/nc
• Date/Publication: 2020-08-10 17:10:17 UTC
• Number of recursive dependencies: 72

Run revdep_details(, "nc") for more info

In both

• checking package dependencies ... NOTE Package suggested but not available for checking: ‘re2r’

nearBynding

• Version: 1.6.0
• GitHub: NA
• Source code: https://github.com/cran/nearBynding
• Date/Publication: 2022-04-26
• Number of recursive dependencies: 126

Run revdep_details(, "nearBynding") for more info

In both

• checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: extdata 6.9Mb

netboost

• Version: 2.4.1
• GitHub: https://github.com/PascalSchlosser/netboost
• Source code: https://github.com/cran/netboost
• Date/Publication: 2022-06-05
• Number of recursive dependencies: 113

Run revdep_details(, "netboost") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘netboost.Rmd’ using rmarkdown Error: processing vignette 'netboost.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘netboost.Rmd’

  SUMMARY: processing the following file failed: ‘netboost.Rmd’

  Error: Vignette re-building failed. Execution halted ```

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

• checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

NPMLEmix

• Version: 1.2
• GitHub: https://github.com/NabarunD/NPMLEmix
• Source code: https://github.com/cran/NPMLEmix
• Date/Publication: 2020-12-06 05:50:02 UTC
• Number of recursive dependencies: 135

Run revdep_details(, "NPMLEmix") for more info

In both

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘CAMAN’ ‘Hmisc’ ‘latexpdf’ ‘spatstat’ All declared Imports should be used.

• checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

numbat

• Version: 1.0.2
• GitHub: https://github.com/kharchenkolab/numbat
• Source code: https://github.com/cran/numbat
• Date/Publication: 2022-09-15 06:10:02 UTC
• Number of recursive dependencies: 178

Run revdep_details(, "numbat") for more info

In both

• checking installed package size ... NOTE installed size is 11.1Mb sub-directories of 1Mb or more: data 4.2Mb libs 6.3Mb

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R.utils’ ‘argparse’ ‘tidyverse’ ‘vcfR’ All declared Imports should be used.

• checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

NxtIRFcore

• Version: 1.2.1
• GitHub: https://github.com/alexchwong/NxtIRFcore
• Source code: https://github.com/cran/NxtIRFcore
• Date/Publication: 2022-06-23
• Number of recursive dependencies: 168

Run revdep_details(, "NxtIRFcore") for more info

In both

• checking installed package size ... NOTE installed size is 13.7Mb sub-directories of 1Mb or more: R 1.6Mb doc 2.4Mb libs 9.0Mb

oce

• Version: 1.7-10
• GitHub: https://github.com/dankelley/oce
• Source code: https://github.com/cran/oce
• Date/Publication: 2022-08-18 17:30:05 UTC
• Number of recursive dependencies: 120

Run revdep_details(, "oce") for more info

In both

• checking installed package size ... NOTE installed size is 16.8Mb sub-directories of 1Mb or more: R 2.6Mb doc 2.0Mb help 3.0Mb libs 7.7Mb

openCyto

• Version: 2.8.4
• GitHub: NA
• Source code: https://github.com/cran/openCyto
• Date/Publication: 2022-07-12
• Number of recursive dependencies: 147

Run revdep_details(, "openCyto") for more info

In both

• checking package dependencies ... NOTE Package suggested but not available for checking: ‘CytoML’

• checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: doc 2.5Mb libs 4.3Mb

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘flowViz’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘flowClust:::.ellipsePoints’ ‘flowStats:::drvkde’ ‘flowWorkspace:::.addGate’ ‘flowWorkspace:::.cpp_addGate’ ‘flowWorkspace:::.cpp_boolGating’ ‘flowWorkspace:::.cpp_setIndices’ ‘flowWorkspace:::.getAllDescendants’ ‘flowWorkspace:::filter_to_list.booleanFilter’ ‘flowWorkspace:::filter_to_list.rectangleGate’ ‘lattice:::updateList’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘groupBy’ ‘isCollapse’ ‘ppMethod’ ‘unlockNamespace’

• checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘openCyto/R/pluginFramework.R’: unlockBinding(methodName, ENV) unlockBinding(methodName, ENV)

• checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘gridExtra’

ORFik

• Version: 1.16.6
• GitHub: https://github.com/Roleren/ORFik
• Source code: https://github.com/cran/ORFik
• Date/Publication: 2022-10-13
• Number of recursive dependencies: 156

Run revdep_details(, "ORFik") for more info

In both

• checking installed package size ... NOTE installed size is 10.8Mb sub-directories of 1Mb or more: doc 4.1Mb libs 3.5Mb

• checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’ ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::normarg_mcols’ ‘biomartr:::getENSEMBL.Seq’ ‘biomartr:::getENSEMBL.gtf’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘find_url_ebi’ ‘revElementsF’ ‘save.fstwig’ ‘trimming.table’

• checking R code for possible problems ... NOTE DEG.plot.static: no visible binding for global variable ‘Regulation’ DEG.plot.static: no visible binding for global variable ‘meanCounts’ DEG.plot.static: no visible binding for global variable ‘LFC’ DTEG.plot: no visible binding for global variable ‘Regulation’ DTEG.plot: no visible binding for global variable ‘rna’ DTEG.plot: no visible binding for global variable ‘rfp’ QCplots: no visible binding for global variable ‘leaders’ QCplots: no visible binding for global variable ‘trailers’ QCstats.plot: no visible binding for global variable ‘variable’ QCstats.plot: no visible binding for global variable ‘sample_total’ ... seq2 seq3 seq4 seq5 size spec spots start1 start2 startCodonCoverage startRegionRelative subtitle sum.count sum_per_gene te trailers upstream_kozak_strength utr3_len utr5_len value variable widths windowMean windowSD zscore Consider adding importFrom("base", "length") importFrom("graphics", "frame") importFrom("stats", "df") importFrom("utils", "head") to your NAMESPACE file.

OSCA.intro

• Version: 1.4.1
• GitHub: https://github.com/OSCA-source/OSCA.intro
• Source code: https://github.com/cran/OSCA.intro
• Date/Publication: 2022-05-23
• Number of recursive dependencies: 199

Run revdep_details(, "OSCA.intro") for more info

In both

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘stub.Rmd’ using rmarkdown [WARNING] This document format requires a nonempty element. Defaulting to 'stub.knit' as the title. To specify a title, use 'title' in metadata or --metadata title="...". --- finished re-building ‘stub.Rmd’</p> <p>"/software/c4/cbi/software/R-4.2.1-gcc10/lib64/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.intro'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)"</p> <p>R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" ...</p> <h1>Execution halted</h1> <p>Error in compileChapter(path) : failed to compile '~/.cache/rebook/OSCA.intro/1.4.1/installation.Rmd' Calls: <Anonymous> ... .precompile_book -> .locked_compile_chapter -> compileChapter Execution halted make: *** [Makefile:4: compiled] Error 1 Error in tools:::buildVignettes(dir = "/c4/home/henrik/repositories/R.utils/revdep/checks/OSCA.intro/new/OSCA.intro.Rcheck/vign_test/OSCA.intro") : running 'make' failed Execution halted ```</p> </li> <li> <p>checking package dependencies ... NOTE <code>Depends: includes the non-default packages: 'batchelor', 'BiocFileCache', 'BiocManager', 'bluster', 'DropletTestFiles', 'DropletUtils', 'gridExtra', 'knitr', 'LoomExperiment', 'R.utils', 'readxl', 'rebook', 'rmarkdown', 'rtracklayer', 'scater', 'scran', 'scRNAseq', 'scuttle', 'SingleCellExperiment', 'uwot', 'zellkonverter' Adding so many packages to the search path is excessive and importing selectively is preferable.</code></p> </li> <li> <p>checking DESCRIPTION meta-information ... NOTE <code>Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocManager’ ‘rmarkdown’ ‘knitr’ A package should be listed in only one of these fields.</code></p> </li> <li> <p>checking for unstated dependencies in vignettes ... NOTE <code>'::' or ':::' import not declared from: ‘BiocStyle’</code></p> </li> </ul> <h1>pagoda2</h1> <p><details></p> <ul> <li>Version: 1.0.10</li> <li>GitHub: https://github.com/kharchenkolab/pagoda2</li> <li>Source code: https://github.com/cran/pagoda2</li> <li>Date/Publication: 2022-04-19 21:40:01 UTC</li> <li>Number of recursive dependencies: 161</li> </ul> <p>Run <code>revdep_details(, "pagoda2")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking installed package size ... NOTE <code>installed size is 10.9Mb sub-directories of 1Mb or more: libs 9.3Mb</code></li> </ul> <h1>paxtoolsr</h1> <p><details></p> <ul> <li>Version: 1.30.0</li> <li>GitHub: https://github.com/BioPAX/paxtoolsr</li> <li>Source code: https://github.com/cran/paxtoolsr</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 163</li> </ul> <p>Run <code>revdep_details(, "paxtoolsr")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking installed package size ... NOTE <code>installed size is 33.8Mb sub-directories of 1Mb or more: doc 1.9Mb extdata 7.3Mb java 24.5Mb</code></p> </li> <li> <p>checking R code for possible problems ... NOTE <code>splitSifnxByPathway: no visible global function definition for ‘%dopar%’ Undefined global functions or variables: %dopar%</code></p> </li> </ul> <h1>PhenotypeSimulator</h1> <p><details></p> <ul> <li>Version: 0.3.4</li> <li>GitHub: https://github.com/HannahVMeyer/PhenotypeSimulator</li> <li>Source code: https://github.com/cran/PhenotypeSimulator</li> <li>Date/Publication: 2021-07-16 13:30:02 UTC</li> <li>Number of recursive dependencies: 102</li> </ul> <p>Run <code>revdep_details(, "PhenotypeSimulator")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking installed package size ... NOTE <code>installed size is 6.0Mb sub-directories of 1Mb or more: doc 1.5Mb extdata 3.1Mb libs 1.2Mb</code></li> </ul> <h1>pmparser</h1> <p><details></p> <ul> <li>Version: 1.0.10</li> <li>GitHub: https://github.com/hugheylab/pmparser</li> <li>Source code: https://github.com/cran/pmparser</li> <li>Date/Publication: 2022-04-27 22:10:08 UTC</li> <li>Number of recursive dependencies: 85</li> </ul> <p>Run <code>revdep_details(, "pmparser")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: Component "major_topic": Lengths (92, 196) differ (string compare on first 92) ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ── keyword_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (18, 37) differ > Component "pmid": Numeric: lengths (18, 37) differ Component "list_owner": Lengths (18, 37) differ (string compare on first 18) ... Attributes: < Component "row.names": Numeric: lengths (28, 74) differ > Component "pmid": Numeric: lengths (28, 74) differ Component "type_name": Lengths (28, 74) differ (string compare on first 28) Component "type_id": Lengths (28, 74) differ (string compare on first 28)</p> <p>[ FAIL 26 | WARN 0 | SKIP 4 | PASS 98 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Execution halted ```</p> </li> </ul> <h1>primirTSS</h1> <p><details></p> <ul> <li>Version: 1.14.0</li> <li>GitHub: https://github.com/ipumin/primirTSS</li> <li>Source code: https://github.com/cran/primirTSS</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 186</li> </ul> <p>Run <code>revdep_details(, "primirTSS")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking dependencies in R code ... WARNING <code>'::' or ':::' import not declared from: 'magrittr'</code></p> </li> <li> <p>checking R code for possible problems ... NOTE <code>check_DHS_df: no visible binding for global variable ‘can_tss’ check_DHS_df: no visible binding for global variable ‘new_info’ check_DHS_s: no visible binding for global variable ‘dhs_p1’ check_DHS_s: no visible binding for global variable ‘dhs_p2’ eponine_score: no visible binding for global variable ‘previous’ eponine_score: no visible binding for global variable ‘histone_p1_flank’ eponine_score: no visible binding for global variable ‘histone_p2_flank’ eponine_score: no visible binding for global variable ‘tss_p1’ ... require_fa: no visible binding for global variable ‘arrow’ tss_filter: no visible binding for global variable ‘gene_id’ tss_filter: no visible binding for global variable ‘new_info’ tss_filter: no visible binding for global variable ‘predicted_tss’ tss_filter: no visible binding for global variable ‘tss_type’ Undefined global functions or variables: TF TF_class arrow can_tss dhs_p1 dhs_p2 e_p_rank end1 eponine_rank gene_id gene_p1 gene_p2 histone_p1_flank histone_p2_flank loci mir_name new_info phast_rank predicted_tss previous seqname start1 stem_loop_p1 stem_loop_p2 symbol_name tss_p1 tss_p2 tss_type</code></p> </li> </ul> <h1>psichomics</h1> <p><details></p> <ul> <li>Version: 1.22.1</li> <li>GitHub: https://github.com/nuno-agostinho/psichomics</li> <li>Source code: https://github.com/cran/psichomics</li> <li>Date/Publication: 2022-07-17</li> <li>Number of recursive dependencies: 254</li> </ul> <p>Run <code>revdep_details(, "psichomics")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking for hidden files and directories ... NOTE <code>Found the following hidden files and directories: .devcontainer These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.</code></p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 9.1Mb sub-directories of 1Mb or more: R 1.5Mb doc 4.5Mb libs 2.0Mb</code></p> </li> </ul> <h1>PubBias</h1> <p><details></p> <ul> <li>Version: 1.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/PubBias</li> <li>Date/Publication: 2013-11-21 06:48:21</li> <li>Number of recursive dependencies: 4</li> </ul> <p>Run <code>revdep_details(, "PubBias")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking DESCRIPTION meta-information ... NOTE <code>Malformed Title field: should not end in a period.</code></p> </li> <li> <p>checking dependencies in R code ... NOTE <code>Packages in Depends field not imported from: ‘R.utils’ ‘rmeta’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.</code></p> </li> </ul> <h1>pubtatordb</h1> <p><details></p> <ul> <li>Version: 0.1.4</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/pubtatordb</li> <li>Date/Publication: 2019-11-22 19:30:02 UTC</li> <li>Number of recursive dependencies: 79</li> </ul> <p>Run <code>revdep_details(, "pubtatordb")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking LazyData ... NOTE <code>'LazyData' is specified without a 'data' directory</code></li> </ul> <h1>pulsedSilac</h1> <p><details></p> <ul> <li>Version: 1.9.1</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/pulsedSilac</li> <li>Date/Publication: 2021-11-21</li> <li>Number of recursive dependencies: 91</li> </ul> <p>Run <code>revdep_details(, "pulsedSilac")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking package dependencies ... ERROR ``` Package required but not available: ‘taRifx’</p> <p>See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```</p> </li> </ul> <h1>PureCN</h1> <p><details></p> <ul> <li>Version: 2.2.0</li> <li>GitHub: https://github.com/lima1/PureCN</li> <li>Source code: https://github.com/cran/PureCN</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 157</li> </ul> <p>Run <code>revdep_details(, "PureCN")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘Quick.Rmd’ using rmarkdown Loading required package: DNAcopy Loading required package: VariantAnnotation Loading required package: BiocGenerics</p> <p>Attaching package: 'BiocGenerics'</p> <p>The following objects are masked from 'package:stats':</p> <p>... l.189 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘PureCN.Rnw’</p> <p>SUMMARY: processing the following file failed: ‘PureCN.Rnw’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> <li> <p>checking package dependencies ... NOTE <code>Package which this enhances but not available for checking: ‘genomicsdb’</code></p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 7.7Mb sub-directories of 1Mb or more: doc 3.5Mb extdata 2.7Mb</code></p> </li> </ul> <h1>QDNAseq</h1> <p><details></p> <ul> <li>Version: 1.32.0</li> <li>GitHub: https://github.com/ccagc/QDNAseq</li> <li>Source code: https://github.com/cran/QDNAseq</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 82</li> </ul> <p>Run <code>revdep_details(, "QDNAseq")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking package dependencies ... NOTE <code>Packages suggested but not available for checking: 'QDNAseq.hg19', 'QDNAseq.mm10'</code></p> </li> <li> <p>checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘QDNAseq.Rnw’ using Sweave EM algorithm started ... </p> <p>Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead.</p> <p>Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. ... l.189 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘QDNAseq.Rnw’</p> <p>SUMMARY: processing the following file failed: ‘QDNAseq.Rnw’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> </ul> <h1>QGameTheory</h1> <p><details></p> <ul> <li>Version: 0.1.2</li> <li>GitHub: https://github.com/indrag49/QGameTheory</li> <li>Source code: https://github.com/cran/QGameTheory</li> <li>Date/Publication: 2020-06-12 08:20:03 UTC</li> <li>Number of recursive dependencies: 20</li> </ul> <p>Run <code>revdep_details(, "QGameTheory")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking LazyData ... NOTE <code>'LazyData' is specified without a 'data' directory</code></li> </ul> <h1>R.devices</h1> <p><details></p> <ul> <li>Version: 2.17.1</li> <li>GitHub: https://github.com/HenrikBengtsson/R.devices</li> <li>Source code: https://github.com/cran/R.devices</li> <li>Date/Publication: 2022-06-21 08:00:02 UTC</li> <li>Number of recursive dependencies: 8</li> </ul> <p>Run <code>revdep_details(, "R.devices")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘R.devices-overview.tex.rsp’ using rsp R.devices v2.17.1 (2022-06-21 08:00:02 UTC) successfully loaded. See ?R.devices for help. Error: processing vignette 'R.devices-overview.tex.rsp' failed with diagnostics: Running 'texi2dvi' on 'R.devices-overview.tex' failed. LaTeX errors: ! Undefined control sequence. l.55 \pdfsuppressptexinfo =-1 ... See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ... <br /> --- failed re-building ‘R.devices-overview.tex.rsp’</p> <p>SUMMARY: processing the following file failed: ‘R.devices-overview.tex.rsp’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> </ul> <h1>R.rsp</h1> <p><details></p> <ul> <li>Version: 0.45.0</li> <li>GitHub: https://github.com/HenrikBengtsson/R.rsp</li> <li>Source code: https://github.com/cran/R.rsp</li> <li>Date/Publication: 2022-06-27 18:30:09 UTC</li> <li>Number of recursive dependencies: 23</li> </ul> <p>Run <code>revdep_details(, "R.rsp")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘R_packages-Static_PDF_and_HTML_vignettes.pdf.asis’ using asis --- finished re-building ‘R_packages-Static_PDF_and_HTML_vignettes.pdf.asis’</p> <p>--- re-building ‘R_packages-LaTeX_vignettes.ltx’ using tex Error: processing vignette 'R_packages-LaTeX_vignettes.ltx' failed with diagnostics: Running 'texi2dvi' on 'R_packages-LaTeX_vignettes.ltx' failed. LaTeX errors: ! Undefined control sequence. l.21 \pdfsuppressptexinfo ... ... <br /> --- failed re-building ‘R_packages-Vignettes_prior_to_R300.tex.rsp’</p> <p>SUMMARY: processing the following files failed: ‘R_packages-LaTeX_vignettes.ltx’ ‘Dynamic_document_creation_using_RSP.tex.rsp’ ‘RSP_refcard.tex.rsp’ ‘R_packages-Vignettes_prior_to_R300.tex.rsp’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> </ul> <h1>rCBA</h1> <p><details></p> <ul> <li>Version: 0.4.3</li> <li>GitHub: https://github.com/jaroslav-kuchar/rCBA</li> <li>Source code: https://github.com/cran/rCBA</li> <li>Date/Publication: 2019-05-29 21:50:03 UTC</li> <li>Number of recursive dependencies: 9</li> </ul> <p>Run <code>revdep_details(, "rCBA")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking LazyData ... NOTE <code>'LazyData' is specified without a 'data' directory</code></li> </ul> <h1>RcisTarget</h1> <p><details></p> <ul> <li>Version: 1.16.0</li> <li>GitHub: https://github.com/aertslab/RcisTarget</li> <li>Source code: https://github.com/cran/RcisTarget</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 146</li> </ul> <p>Run <code>revdep_details(, "RcisTarget")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking whether package ‘RcisTarget’ can be installed ... ERROR <code>Installation failed. See ‘/c4/home/henrik/repositories/R.utils/revdep/checks/RcisTarget/new/RcisTarget.Rcheck/00install.out’ for details.</code></p> </li> <li> <p>checking package dependencies ... NOTE <code>Packages which this enhances but not available for checking: 'doMC', 'doRNG', 'zoo'</code></p> </li> </ul> <h2>Installation</h2> <h3>Devel</h3> <pre><code>* installing *source* package ‘RcisTarget’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading sh: line 1: 36705 Illegal instruction (core dumped) R_TESTS= '/software/c4/cbi/software/R-4.2.1-gcc10/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/scratch/henrik/Rtmp9Yw4QD/file8f5b641b179d' *** caught illegal operation *** address 0x2acb618a32e7, cause 'illegal operand' ... 4: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 6: loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, partial = TRUE) 7: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage")) 8: suppressPackageStartupMessages(loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, partial = TRUE)) 9: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, compress = compress, set.install.dir = set.install.dir) 10: tools:::makeLazyLoading("RcisTarget", "/c4/home/henrik/repositories/R.utils/revdep/checks/RcisTarget/new/RcisTarget.Rcheck/00LOCK-RcisTarget/00new", keep.source = FALSE, keep.parse.data = FALSE, set.install.dir = "/c4/home/henrik/repositories/R.utils/revdep/checks/RcisTarget/new/RcisTarget.Rcheck/RcisTarget") An irrecoverable exception occurred. R is aborting now ... ERROR: lazy loading failed for package ‘RcisTarget’ * removing ‘/c4/home/henrik/repositories/R.utils/revdep/checks/RcisTarget/new/RcisTarget.Rcheck/RcisTarget’ </code></pre> <h3>CRAN</h3> <pre><code>* installing *source* package ‘RcisTarget’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading sh: line 1: 36634 Illegal instruction (core dumped) R_TESTS= '/software/c4/cbi/software/R-4.2.1-gcc10/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/scratch/henrik/Rtmpu6NOaM/file8f1475564b2e' *** caught illegal operation *** address 0x2b21e03252e7, cause 'illegal operand' ... 4: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 6: loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, partial = TRUE) 7: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage")) 8: suppressPackageStartupMessages(loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, partial = TRUE)) 9: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, compress = compress, set.install.dir = set.install.dir) 10: tools:::makeLazyLoading("RcisTarget", "/c4/home/henrik/repositories/R.utils/revdep/checks/RcisTarget/old/RcisTarget.Rcheck/00LOCK-RcisTarget/00new", keep.source = FALSE, keep.parse.data = FALSE, set.install.dir = "/c4/home/henrik/repositories/R.utils/revdep/checks/RcisTarget/old/RcisTarget.Rcheck/RcisTarget") An irrecoverable exception occurred. R is aborting now ... ERROR: lazy loading failed for package ‘RcisTarget’ * removing ‘/c4/home/henrik/repositories/R.utils/revdep/checks/RcisTarget/old/RcisTarget.Rcheck/RcisTarget’ </code></pre> <h1>Rcwl</h1> <p><details></p> <ul> <li>Version: 1.12.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/Rcwl</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 127</li> </ul> <p>Run <code>revdep_details(, "Rcwl")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking for hidden files and directories ... NOTE <code>Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.</code></p> </li> <li> <p>checking whether package ‘Rcwl’ can be installed ... NOTE <code>Found the following notes/warnings: Non-staged installation was used See ‘/c4/home/henrik/repositories/R.utils/revdep/checks/Rcwl/new/Rcwl.Rcheck/00install.out’ for details.</code></p> </li> </ul> <h1>rddapp</h1> <p><details></p> <ul> <li>Version: 1.3.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/rddapp</li> <li>Date/Publication: 2022-02-13 18:50:02 UTC</li> <li>Number of recursive dependencies: 146</li> </ul> <p>Run <code>revdep_details(, "rddapp")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking whether package ‘rddapp’ can be installed ... WARNING <code>Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/R.utils/revdep/checks/rddapp/new/rddapp.Rcheck/00install.out’ for details.</code></li> </ul> <h1>rdwd</h1> <p><details></p> <ul> <li>Version: 1.6.0</li> <li>GitHub: https://github.com/brry/rdwd</li> <li>Source code: https://github.com/cran/rdwd</li> <li>Date/Publication: 2022-05-30 09:40:02 UTC</li> <li>Number of recursive dependencies: 157</li> </ul> <p>Run <code>revdep_details(, "rdwd")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking installed package size ... NOTE <code>installed size is 5.5Mb sub-directories of 1Mb or more: R 3.7Mb data 1.4Mb</code></li> </ul> <h1>recountmethylation</h1> <p><details></p> <ul> <li>Version: 1.6.1</li> <li>GitHub: https://github.com/metamaden/recountmethylation</li> <li>Source code: https://github.com/cran/recountmethylation</li> <li>Date/Publication: 2022-05-29</li> <li>Number of recursive dependencies: 186</li> </ul> <p>Run <code>revdep_details(, "recountmethylation")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking examples ... ERROR ``` Running examples in ‘recountmethylation-Ex.R’ failed The error most likely occurred in:</p> <blockquote> <h3>Name: get_qcsignal</h3> <h3>Title: get_qcsignal</h3> <h3>Aliases: get_qcsignal</h3> <h3>** Examples</h3> <p>library(minfiData) Error in library(minfiData) : there is no package called ‘minfiData’ Execution halted ```</p> </blockquote> </li> <li> <p>checking re-building of vignette outputs ... ERROR <code>`` Error(s) in re-building vignettes: --- re-building ‘recountmethylation_data_analyses.Rmd’ using rmarkdown Warning in eval(expr, envir, enclos) : NAs introduced by coercion Warning in cor.test.default(mdf$predage, mdf$chron.age, method = "spearman") : Cannot compute exact p-value with ties The magick package is required to crop "/c4/home/henrik/repositories/R.utils/revdep/checks/recountmethylation/new/recountmethylation.Rcheck/vign_test/recountmethylation/vignettes/recountmethylation_data_analyses_files/figure-html/unnamed-chunk-13-1.png" but not available.</code>geom_smooth()` using formula 'y ~ x' The magick package is required to crop "/c4/home/henrik/repositories/R.utils/revdep/checks/recountmethylation/new/recountmethylation.Rcheck/vign_test/recountmethylation/vignettes/recountmethylation_data_analyses_files/figure-html/unnamed-chunk-14-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/R.utils/revdep/checks/recountmethylation/new/recountmethylation.Rcheck/vign_test/recountmethylation/vignettes/recountmethylation_data_analyses_files/figure-html/unnamed-chunk-21-1.png" but not available. Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) : ... Error: processing vignette 'recountmethylation_users_guide.Rmd' failed with diagnostics: cannot load annotation package IlluminaHumanMethylation450kanno.ilmn12.hg19 --- failed re-building ‘recountmethylation_users_guide.Rmd’</p> <p>SUMMARY: processing the following files failed: ‘recountmethylation_search_index.Rmd’ ‘recountmethylation_users_guide.Rmd’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> <li> <p>checking dependencies in R code ... WARNING <code>'::' or ':::' imports not declared from: ‘DelayedMatrixStats’ ‘basilisk’ ‘reticulate’ Namespace in Imports field not imported from: ‘IlluminaHumanMethylation450kmanifest’ All declared Imports should be used. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘ba.background’ ‘ba.biotinstaining.grn’ ‘ba.biotinstaining.red’ ‘ba.bisulfiteconv1.grn’ ‘ba.bisulfiteconv1.red’ ‘ba.bisulfiteconv2’ ‘ba.extension.grn’ ‘ba.extension.red’ ‘ba.hybridization.hi.vs.med’ ‘ba.hybridization.med.vs.low’ ‘ba.nonpolymorphic.grn’ ‘ba.nonpolymorphic.red’ ‘ba.restoration’ ‘ba.specificity1.grn’ ‘ba.specificity1.red’ ‘ba.specificity2’ ‘ba.targetremoval1’ ‘ba.targetremoval2’ ‘setup_sienv’</code></p> </li> <li> <p>checking for unstated dependencies in examples ... WARNING <code>'library' or 'require' call not declared from: ‘minfiData’</code></p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 9.4Mb sub-directories of 1Mb or more: doc 4.1Mb extdata 5.1Mb</code></p> </li> <li> <p>checking R code for possible problems ... NOTE <code>get_fh : <anonymous>: no visible global function definition for ‘make_fhmatrix_autolabel’ make_si : <anonymous>: no visible global function definition for ‘make_hnsw_si’ query_si: no visible binding for global variable ‘v’ query_si : <anonymous>: no visible global function definition for ‘make_dfk_sampleid’ Undefined global functions or variables: make_dfk_sampleid make_fhmatrix_autolabel make_hnsw_si v</code></p> </li> <li> <p>checking Rd files ... NOTE <code>prepare_Rd: query_si.Rd:33-35: Dropping empty section \value</code></p> </li> <li> <p>checking for unstated dependencies in vignettes ... NOTE <code>'library' or 'require' calls not declared from: ‘basilisk’ ‘reticulate’</code></p> </li> </ul> <h1>regtools</h1> <p><details></p> <ul> <li>Version: 1.7.0</li> <li>GitHub: https://github.com/matloff/regtools</li> <li>Source code: https://github.com/cran/regtools</li> <li>Date/Publication: 2022-03-30 17:30:02 UTC</li> <li>Number of recursive dependencies: 156</li> </ul> <p>Run <code>revdep_details(, "regtools")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking package dependencies ... NOTE <code>Packages suggested but not available for checking: 'cdparcoord', 'partools'</code></li> </ul> <h1>ReportingTools</h1> <p><details></p> <ul> <li>Version: 2.36.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/ReportingTools</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 190</li> </ul> <p>Run <code>revdep_details(, "ReportingTools")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking R code for possible problems ... NOTE <code>.GeneSetCollection.to.data.frame: no visible binding for global variable 'description' .GeneSetCollection.to.html: no visible binding for global variable 'description' .GeneSetCollection.to.html2: no visible binding for global variable 'description' .PFAMhyperG.to.html: no visible binding for global variable 'keytype' .PFAMhyperG.to.html: no visible binding for global variable 'columns' .make.gene.plots: no visible global function definition for 'exprs' .marrayLM.to.data.frame: no visible global function definition for ... custHeaderPanel: no visible global function definition for 'tag' custHeaderPanel: no visible global function definition for 'div' custHeaderPanel: no visible global function definition for 'h1' publish,trellis-HTMLReport: no visible binding for global variable 'htmlRep' toReportDF,DESeqDataSet: no visible global function definition for 'mcols' Undefined global functions or variables: HTML columns description div exprs fData featureNames h1 htmlRep keys keytype mcols org.Hs.eg.db tag tagList tags</code></li> </ul> <h1>RforProteomics</h1> <p><details></p> <ul> <li>Version: 1.34.1</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/RforProteomics</li> <li>Date/Publication: 2022-09-01</li> <li>Number of recursive dependencies: 276</li> </ul> <p>Run <code>revdep_details(, "RforProteomics")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘RProtVis.Rmd’ using rmarkdown Loading required package: MSnbase Loading required package: BiocGenerics</p> <p>Attaching package: 'BiocGenerics'</p> <p>The following objects are masked from 'package:stats':</p> <pre><code>IQR, mad, sd, var, xtabs </code></pre> <p>... Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics: Can not open file /c4/home/henrik/.cache/R/rpx/9cda763ac7f8_TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML! Original error was: Error in pwizModule$open(filename): [SAXParser::parse()] Empty tag at offset 182886312.</p> <p>--- failed re-building ‘RforProteomics.Rmd’</p> <p>SUMMARY: processing the following files failed: ‘RProtVis.Rmd’ ‘RforProteomics.Rmd’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> <li> <p>checking whether package ‘RforProteomics’ can be installed ... WARNING <code>Found the following significant warnings: Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’ See ‘/c4/home/henrik/repositories/R.utils/revdep/checks/RforProteomics/new/RforProteomics.Rcheck/00install.out’ for details.</code></p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 10.4Mb sub-directories of 1Mb or more: doc 9.6Mb</code></p> </li> </ul> <h1>RLSeq</h1> <p><details></p> <ul> <li>Version: 1.2.0</li> <li>GitHub: https://github.com/Bishop-Laboratory/RLSeq</li> <li>Source code: https://github.com/cran/RLSeq</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 231</li> </ul> <p>Run <code>revdep_details(, "RLSeq")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking tests ... <code>`` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: see ?RLHub and browseVignettes('RLHub') for documentation see ?RLHub and browseVignettes('RLHub') for documentation see ?RLHub and browseVignettes('RLHub') for documentation see ?RLHub and browseVignettes('RLHub') for documentation [1] "Note: The minimum p-value with only 10 permutations is 0.0909090909090909. You should consider increasing the number of permutations." see ?RLHub and browseVignettes('RLHub') for documentation ... warns\[1\] does not match "User-supplied sample test value is NA for .*". Actual value: "Use of \.data in tidyselect expressions was deprecated in tidyselect 1\.2\.0\.\\ni Please use</code>"db"<code>instead of</code>.data\$db`" Backtrace: ▆</p> <ol> <li>└─testthat::expect_match(warns[1], regexp = "User-supplied sample test value is NA for .*") at test-plotEnrichment.R:15:4</li> <li>└─testthat:::expect_match_(...)</li> </ol> <p>[ FAIL 1 | WARN 116 | SKIP 0 | PASS 6 ] Error: Test failures Execution halted ```</p> </li> </ul> <h1>RMassBank</h1> <p><details></p> <ul> <li>Version: 3.6.1</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/RMassBank</li> <li>Date/Publication: 2022-05-31</li> <li>Number of recursive dependencies: 171</li> </ul> <p>Run <code>revdep_details(, "RMassBank")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking package dependencies ... ERROR ``` Package required but not available: ‘ChemmineOB’</p> <p>See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```</p> </li> </ul> <h1>RNAseq123</h1> <p><details></p> <ul> <li>Version: 1.20.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/RNAseq123</li> <li>Date/Publication: 2022-04-29</li> <li>Number of recursive dependencies: 158</li> </ul> <p>Run <code>revdep_details(, "RNAseq123")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘designmatrices.Rmd’ using rmarkdown Quitting from lines 94-95 (designmatrices.Rmd) Error: processing vignette 'designmatrices.Rmd' failed with diagnostics: there is no package called 'here' --- failed re-building ‘designmatrices.Rmd’</p> <p>--- re-building ‘limmaWorkflow.Rmd’ using rmarkdown Loading required package: AnnotationDbi Loading required package: stats4 ... The magick package is required to crop "/c4/home/henrik/repositories/R.utils/revdep/checks/RNAseq123/new/RNAseq123.Rcheck/vign_test/RNAseq123/vignettes/limmaWorkflow_CHN_files/figure-html/venn-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/R.utils/revdep/checks/RNAseq123/new/RNAseq123.Rcheck/vign_test/RNAseq123/vignettes/limmaWorkflow_CHN_files/figure-html/heatmap-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/R.utils/revdep/checks/RNAseq123/new/RNAseq123.Rcheck/vign_test/RNAseq123/vignettes/limmaWorkflow_CHN_files/figure-html/barcodeplot-1.png" but not available. --- finished re-building ‘limmaWorkflow_CHN.Rmd’</p> <p>SUMMARY: processing the following file failed: ‘designmatrices.Rmd’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> <li> <p>checking package dependencies ... NOTE <code>Depends: includes the non-default packages: 'Glimma', 'limma', 'edgeR', 'gplots', 'RColorBrewer', 'Mus.musculus', 'R.utils', 'TeachingDemos', 'statmod', 'BiocWorkflowTools' Adding so many packages to the search path is excessive and importing selectively is preferable.</code></p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 8.2Mb sub-directories of 1Mb or more: doc 6.1Mb extdata 2.1Mb</code></p> </li> <li> <p>checking for unstated dependencies in vignettes ... NOTE <code>'::' or ':::' import not declared from: ‘here’</code></p> </li> </ul> <h1>ruta</h1> <p><details></p> <ul> <li>Version: 1.1.0</li> <li>GitHub: https://github.com/fdavidcl/ruta</li> <li>Source code: https://github.com/cran/ruta</li> <li>Date/Publication: 2019-03-18 13:10:02 UTC</li> <li>Number of recursive dependencies: 70</li> </ul> <p>Run <code>revdep_details(, "ruta")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking LazyData ... NOTE <code>'LazyData' is specified without a 'data' directory</code></li> </ul> <h1>rutifier</h1> <p><details></p> <ul> <li>Version: 1.0.4</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/rutifier</li> <li>Date/Publication: 2020-03-02 09:50:02 UTC</li> <li>Number of recursive dependencies: 3</li> </ul> <p>Run <code>revdep_details(, "rutifier")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking LazyData ... NOTE <code>'LazyData' is specified without a 'data' directory</code></li> </ul> <h1>signatureSearchData</h1> <p><details></p> <ul> <li>Version: 1.10.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/signatureSearchData</li> <li>Date/Publication: 2022-04-28</li> <li>Number of recursive dependencies: 98</li> </ul> <p>Run <code>revdep_details(, "signatureSearchData")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking dependencies in R code ... NOTE <code>Namespaces in Imports field not imported from: ‘ExperimentHub’ ‘rhdf5’ All declared Imports should be used.</code></li> </ul> <h1>simpleSingleCell</h1> <p><details></p> <ul> <li>Version: 1.20.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/simpleSingleCell</li> <li>Date/Publication: 2022-04-29</li> <li>Number of recursive dependencies: 151</li> </ul> <p>Run <code>revdep_details(, "simpleSingleCell")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking examples ... ERROR ``` Running examples in ‘simpleSingleCell-Ex.R’ failed The error most likely occurred in:</p> <blockquote> <h3>Name: chapterPreamble</h3> <h3>Title: Execute chapter preamble code</h3> <h3>Aliases: chapterPreamble</h3> <h3>** Examples</h3> <p>tmp <- tempfile(fileext=".Rmd") ... processing file: file2e2b17189046.Rmd label: unnamed-chunk-1 (with options) List of 2 $ echo : logi FALSE $ results: chr "asis"</p> </blockquote> <p>Quitting from lines 2-3 (file2e2b17189046.Rmd) Error in loadNamespace(x) : there is no package called 'rebook' Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ```</p> </li> <li> <p>checking for hidden files and directories ... NOTE <code>Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.</code></p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 7.9Mb sub-directories of 1Mb or more: doc 7.9Mb</code></p> </li> <li> <p>checking dependencies in R code ... NOTE <code>Namespace in Imports field not imported from: ‘BiocStyle’ All declared Imports should be used.</code></p> </li> </ul> <h1>systemPipeShiny</h1> <p><details></p> <ul> <li>Version: 1.6.1</li> <li>GitHub: https://github.com/systemPipeR/systemPipeShiny</li> <li>Source code: https://github.com/cran/systemPipeShiny</li> <li>Date/Publication: 2022-05-26</li> <li>Number of recursive dependencies: 201</li> </ul> <p>Run <code>revdep_details(, "systemPipeShiny")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking installed package size ... NOTE <code>installed size is 5.4Mb sub-directories of 1Mb or more: doc 3.8Mb</code></p> </li> <li> <p>checking R code for possible problems ... NOTE <code>core_topServer : module : <anonymous>: warning in eval(code, env = .GlobalEnv): partial argument match of 'env' to 'envir' .validateGuide: no visible binding for global variable ‘guide_ui’ .validateGuide: no visible binding for global variable ‘guide_content’ .validateGuide : <anonymous>: no visible binding for global variable ‘guide_content’ admin_infoServer : timeDiffString: no visible binding for global variable ‘time_start’ admin_infoServer : getCPU: no visible binding for global variable ‘V2’ appLoadingTime: no visible binding for global variable ‘time_start’ ... .cur_plot .plot_num .rs_dir PC1 PC2 Sample V2 X1 X2 baseMean cmp dev.control dev.cur dev.new dev.off dim1 dim2 direction guide_content guide_ui hcl.colors input_code log2FoldChange padj pass_filter png recordPlot replayPlot session spsRNA_trans tab_file_name tab_info time_start title trans_table type Consider adding importFrom("grDevices", "dev.control", "dev.cur", "dev.new", "dev.off", "hcl.colors", "png", "recordPlot", "replayPlot") importFrom("graphics", "title") to your NAMESPACE file.</code></p> </li> </ul> <h1>tablet</h1> <p><details></p> <ul> <li>Version: 0.5.8</li> <li>GitHub: https://github.com/bergsmat/tablet</li> <li>Source code: https://github.com/cran/tablet</li> <li>Date/Publication: 2022-04-29 22:50:02 UTC</li> <li>Number of recursive dependencies: 128</li> </ul> <p>Run <code>revdep_details(, "tablet")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘tablet-introduction-html.Rmd’ using rmarkdown --- finished re-building ‘tablet-introduction-html.Rmd’</p> <p>--- re-building ‘tablet-introduction-pdf.Rmd’ using rmarkdown A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois").</p> <p>tlmgr: Local TeX Live (2021) is older than remote repository (2022). Cross release updates are only supported with update-tlmgr-latest(.sh/.exe) --update ...</p> <p>Error: processing vignette 'tablet-introduction-pdf.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/R.utils/revdep/checks/tablet/new/tablet.Rcheck/vign_test/tablet/vignettes/tablet-introduction-pdf.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See tablet-introduction-pdf.log for more info. --- failed re-building ‘tablet-introduction-pdf.Rmd’</p> <p>SUMMARY: processing the following file failed: ‘tablet-introduction-pdf.Rmd’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> <li> <p>checking Rd cross-references ... NOTE <code>Package unavailable to check Rd xrefs: ‘foreign’</code></p> </li> </ul> <h1>TCGAbiolinks</h1> <p><details></p> <ul> <li>Version: 2.24.3</li> <li>GitHub: https://github.com/BioinformaticsFMRP/TCGAbiolinks</li> <li>Source code: https://github.com/cran/TCGAbiolinks</li> <li>Date/Publication: 2022-06-16</li> <li>Number of recursive dependencies: 346</li> </ul> <p>Run <code>revdep_details(, "TCGAbiolinks")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking dependencies in R code ... WARNING <code>'library' or 'require' call not declared from: ‘dplyr’ 'library' or 'require' calls in package code: ‘dplyr’ ‘maftools’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.</code></p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 107.1Mb sub-directories of 1Mb or more: R 1.6Mb data 4.5Mb doc 100.8Mb</code></p> </li> <li> <p>checking R code for possible problems ... NOTE <code>GDCquery : <anonymous>: no visible binding for global variable ‘submitter_id’ GDCquery : <anonymous>: no visible binding for global variable ‘is_ffpe’ TCGAanalyze_DEA: no visible binding for global variable ‘barcode’ TCGAanalyze_DEA: no visible binding for global variable ‘clinical’ TCGAquery_recount2: no visible binding for global variable ‘rse_gene’ TCGAtumor_purity: no visible binding for global variable ‘Tumor.purity’ TCGAvisualize_oncoprint: no visible binding for global variable ‘value’ TCGAvisualize_starburst: no visible binding for global variable ... readGeneExpressionQuantification : <anonymous>: no visible binding for '<<-' assignment to ‘assay.list’ readGeneExpressionQuantification: no visible binding for global variable ‘assay.list’ readSingleCellAnalysis : <anonymous>: no visible global function definition for ‘Read10X’ Undefined global functions or variables: Read10X Tumor.purity assay.list barcode clinical coordinates exon geFDR2 gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id sample_type starburst.status submitter_id threshold.starburst value</code></p> </li> <li> <p>checking for unstated dependencies in vignettes ... NOTE <code>'::' or ':::' import not declared from: ‘DT’ 'library' or 'require' call not declared from: ‘DT’</code></p> </li> </ul> <h1>TCGAutils</h1> <p><details></p> <ul> <li>Version: 1.16.1</li> <li>GitHub: https://github.com/waldronlab/TCGAutils</li> <li>Source code: https://github.com/cran/TCGAutils</li> <li>Date/Publication: 2022-10-11</li> <li>Number of recursive dependencies: 224</li> </ul> <p>Run <code>revdep_details(, "TCGAutils")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking examples ... ERROR ``` Running examples in ‘TCGAutils-Ex.R’ failed The error most likely occurred in:</p> <blockquote> <h3>Name: getFileName</h3> <h3>Title: Find the file names used in RTCGAToolbox</h3> <h3>Aliases: getFileName</h3> <h3>** Examples</h3> <p>getFileName("COAD", dataType = "CNASNP") Error in open.connection(x, "rb") : HTTP error 503. Calls: getFileName -> <Anonymous> -> read_html.default Execution halted ```</p> </blockquote> </li> <li> <p>checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘TCGAutils.Rmd’ using rmarkdown Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats</p> <p>Attaching package: 'MatrixGenerics'</p> <p>The following objects are masked from 'package:matrixStats': ... Quitting from lines 41-48 (TCGAutils.Rmd) Error: processing vignette 'TCGAutils.Rmd' failed with diagnostics: there is no package called 'RTCGAToolbox' --- failed re-building ‘TCGAutils.Rmd’</p> <p>SUMMARY: processing the following file failed: ‘TCGAutils.Rmd’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> <li> <p>checking package dependencies ... NOTE <code>Package suggested but not available for checking: ‘RTCGAToolbox’</code></p> </li> <li> <p>checking dependencies in R code ... NOTE <code>Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘GenomicRanges:::.normarg_field’ ‘S4Vectors:::selectSome’ See the note in ?`:::` about the use of this operator.</code></p> </li> <li> <p>checking Rd cross-references ... NOTE <code>Package unavailable to check Rd xrefs: ‘RTCGAToolbox’</code></p> </li> </ul> <h1>TFEA.ChIP</h1> <p><details></p> <ul> <li>Version: 1.16.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/TFEA.ChIP</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 163</li> </ul> <p>Run <code>revdep_details(, "TFEA.ChIP")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking tests ... ``` Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Complete output: > BiocGenerics:::testPackage(pkgname = "TFEA.ChIP")</p> <p>Because of space limitations, TFEA.ChIPs internal database only includes ChIP-seq experiments from cell types in ENCODE's tiers 1, 2, and 2.5. To download the full ReMap2022 database, as well as other ready-to-use databases, visit https://github.com/LauraPS1/TFEA.ChIP_downloads Error in library("RUnit", quietly = TRUE) : there is no package called 'RUnit' Calls: <Anonymous> -> library Execution halted ```</p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 5.4Mb sub-directories of 1Mb or more: data 4.9Mb</code></p> </li> <li> <p>checking R code for possible problems ... NOTE <code>rankTFs: no visible binding for global variable ‘arg.ES’ rankTFs: no visible binding for global variable ‘ES’ rankTFs: no visible binding for global variable ‘TF’ Undefined global functions or variables: ES TF arg.ES</code></p> </li> </ul> <h1>tmle.npvi</h1> <p><details></p> <ul> <li>Version: 0.10.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/tmle.npvi</li> <li>Date/Publication: 2015-05-22 18:59:02</li> <li>Number of recursive dependencies: 41</li> </ul> <p>Run <code>revdep_details(, "tmle.npvi")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking re-building of vignette outputs ... WARNING <code>`` Error(s) in re-building vignettes: ... --- re-building ‘tmle-npvi.Rnw’ using knitr Error: processing vignette 'tmle-npvi.Rnw' failed with diagnostics: Running 'texi2dvi' on 'tmle-npvi.tex' failed. LaTeX errors: ! LaTeX Error: File</code>manfnt.sty' not found.</p> <p>Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) ... l.59 \usepackage [textwidth=15cm, textheight=23cm]{geometry}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘tmle-npvi.Rnw’</p> <p>SUMMARY: processing the following file failed: ‘tmle-npvi.Rnw’</p> <p>Error: Vignette re-building failed. Execution halted ```</p> </li> <li> <p>checking R code for possible problems ... NOTE <code>NPVI: no visible global function definition for ‘quantile’ SL.glm.condExpX2givenW: no visible global function definition for ‘as.formula’ SL.glm.condExpX2givenW: no visible global function definition for ‘glm’ SL.glm.condExpXYgivenW: no visible global function definition for ‘as.formula’ SL.glm.condExpXYgivenW: no visible global function definition for ‘glm’ SL.glm.g: no visible global function definition for ‘as.formula’ SL.glm.g: no visible global function definition for ‘glm’ SL.glm.theta: no visible global function definition for ‘as.formula’ ... as.formula binomial dnorm gaussian glm head integrate model.matrix optimize plogis pnorm qlogis qnorm quantile rnorm runif sd str tail update var Consider adding importFrom("stats", "as.formula", "binomial", "dnorm", "gaussian", "glm", "integrate", "model.matrix", "optimize", "plogis", "pnorm", "qlogis", "qnorm", "quantile", "rnorm", "runif", "sd", "update", "var") importFrom("utils", "head", "str", "tail") to your NAMESPACE file.</code></p> </li> </ul> <h1>TraRe</h1> <p><details></p> <ul> <li>Version: 1.4.0</li> <li>GitHub: https://github.com/ubioinformat/TraRe</li> <li>Source code: https://github.com/cran/TraRe</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 96</li> </ul> <p>Run <code>revdep_details(, "TraRe")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking installed package size ... NOTE <code>installed size is 6.6Mb sub-directories of 1Mb or more: doc 2.0Mb extdata 4.4Mb</code></li> </ul> <h1>Ularcirc</h1> <p><details></p> <ul> <li>Version: 1.14.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/Ularcirc</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 155</li> </ul> <p>Run <code>revdep_details(, "Ularcirc")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'Junction_Sequence_from_Genome' ‘SelectUniqueJunct_Value’ Documented arguments not in \usage in documentation object 'Junction_Sequence_from_Genome': ‘SelectUniqueJunct_value’</p> <p>Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```</p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 5.8Mb sub-directories of 1Mb or more: doc 1.1Mb extdata 4.4Mb</code></p> </li> <li> <p>checking dependencies in R code ... NOTE <code>Namespaces in Imports field not imported from: ‘DT’ ‘GenomeInfoDb’ ‘GenomeInfoDbData’ ‘Organism.dplyr’ ‘ggplot2’ ‘ggrepel’ ‘mirbase.db’ ‘moments’ ‘shinyFiles’ ‘shinydashboard’ ‘shinyjs’ ‘yaml’ All declared Imports should be used.</code></p> </li> <li> <p>checking R code for possible problems ... NOTE <code>FilterChimericJuncs: no visible global function definition for ‘Filter_by_Data_Set’ FilterChimericJuncs: no visible binding for global variable ‘strandDonor’ FilterChimericJuncs: no visible binding for global variable ‘startDonor’ FilterChimericJuncs: no visible binding for global variable ‘startAcceptor’ Junction_Sequence_from_Genome: no visible global function definition for ‘extractGenomeSequence’ ... ‘BSjuncName’ SelectUniqueJunctions: no visible binding for global variable ‘JuncType’ SelectUniqueJunctions: no visible binding for global variable ‘strandDonor’ loadSTAR_chimeric: no visible binding for global variable ‘..returnColIdx’ Undefined global functions or variables: . ..returnColIdx BSjuncName Filter_by_Data_Set JuncType extractGenomeSequence startAcceptor startDonor strandDonor</code></p> </li> </ul> <h1>understandBPMN</h1> <p><details></p> <ul> <li>Version: 1.1.1</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/understandBPMN</li> <li>Date/Publication: 2019-09-27 11:30:03 UTC</li> <li>Number of recursive dependencies: 103</li> </ul> <p>Run <code>revdep_details(, "understandBPMN")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking LazyData ... NOTE <code>'LazyData' is specified without a 'data' directory</code></li> </ul> <h1>Uniquorn</h1> <p><details></p> <ul> <li>Version: 2.16.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/Uniquorn</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 122</li> </ul> <p>Run <code>revdep_details(, "Uniquorn")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking dependencies in R code ... WARNING <code>Missing or unexported object: ‘GenomicRanges::GenomicRangesList’</code></p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 7.6Mb sub-directories of 1Mb or more: extdata 6.5Mb</code></p> </li> <li> <p>checking DESCRIPTION meta-information ... NOTE <code>Malformed Description field: should contain one or more complete sentences.</code></p> </li> <li> <p>checking R code for possible problems ... NOTE <code>add_p_q_values_statistics: no visible binding for '<<-' assignment to ‘sig_vec’ add_p_q_values_statistics: no visible binding for global variable ‘sig_vec’ create_bed_file: no visible binding for global variable ‘res_table’ create_bed_file: no visible binding for global variable ‘sim_list’ identify_vcf_file: no visible binding for global variable ‘vcf_fingerprint’ identify_vcf_file: no visible binding for global variable ‘output_file_xls’ ... assignment to ‘g_mat_exclude’ write_w0_and_split_w0_into_lower_weights: no visible binding for global variable ‘g_mat_exclude’ Undefined global functions or variables: .SD Index Tumor_Sample_Barcode ccls_all data.table fread g_mat_exclude output_file_xls position res_table sig_vec sim_list tail vcf_fingerprint Consider adding importFrom("utils", "tail") to your NAMESPACE file.</code></p> </li> </ul> <h1>ViSEAGO</h1> <p><details></p> <ul> <li>Version: 1.10.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/ViSEAGO</li> <li>Date/Publication: 2022-04-26</li> <li>Number of recursive dependencies: 162</li> </ul> <p>Run <code>revdep_details(, "ViSEAGO")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li> <p>checking whether package ‘ViSEAGO’ can be installed ... WARNING <code>Found the following significant warnings: Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ See ‘/c4/home/henrik/repositories/R.utils/revdep/checks/ViSEAGO/new/ViSEAGO.Rcheck/00install.out’ for details.</code></p> </li> <li> <p>checking dependencies in R code ... WARNING <code>'library' or 'require' call not declared from: ‘topGO’ 'library' or 'require' call to ‘topGO’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘processx’ All declared Imports should be used.</code></p> </li> <li> <p>checking data for ASCII and uncompressed saves ... WARNING ```</p> <p>Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress myGOs.RData 876Kb 517Kb xz ```</p> </li> <li> <p>checking installed package size ... NOTE <code>installed size is 16.5Mb sub-directories of 1Mb or more: doc 4.3Mb extdata 10.6Mb</code></p> </li> <li> <p>checking R code for possible problems ... NOTE <code>annotate,character-genomic_ressource: warning in getBM(attributes = c("ensembl_gene_id", "go_id", "go_linkage_type", "namespace_1003"), filters = unlist(go_filter[grep("with GO ID", ignore.case = TRUE, go_filter$description), "name", with = FALSE]), value = TRUE, mart = myspecies): partial argument match of 'value' to 'values' compute_SS_distances,ANY-character: warning in select(GO.db, keys = onto$values, column = "TERM"): partial argument match of 'column' to 'columns' merge_enrich_terms,list : genes_symbols_add: warning in getBM(attributes = c("ensembl_gene_id", "external_gene_name"), value ... ‘pathway’ Undefined global functions or variables: . ENTREZID ES EVIDENCE GO GO.ID GO.cluster IC Id N NES ONTOLOGY Significant_genes dev.off end genes_frequency leadingEdge log2err nMoreExtreme padj pathway png pval size start text Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "text") importFrom("stats", "end", "start") to your NAMESPACE file.</code></p> </li> </ul> <h1>wrProteo</h1> <p><details></p> <ul> <li>Version: 1.6.0</li> <li>GitHub: NA</li> <li>Source code: https://github.com/cran/wrProteo</li> <li>Date/Publication: 2022-03-01 17:30:02 UTC</li> <li>Number of recursive dependencies: 58</li> </ul> <p>Run <code>revdep_details(, "wrProteo")</code> for more info</p> <p></details></p> <h2>In both</h2> <ul> <li>checking installed package size ... NOTE <code>installed size is 6.2Mb sub-directories of 1Mb or more: doc 3.3Mb extdata 2.4Mb</code></li> </ul>

HenrikBengtsson/R.utils documentation built on March 7, 2024, 9:37 a.m.