revdep/problems.md

In HenrikBengtsson/R.oo: R Object-Oriented Programming with or without References

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.oo/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’

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.

bioCancer

• Version: 1.24.01
• GitHub: https://github.com/kmezhoud/bioCancer
• Source code: https://github.com/cran/bioCancer
• Date/Publication: 2022-04-27
• Number of recursive dependencies: 220

Run revdep_details(, "bioCancer") for more info

In both

• checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: app 3.2Mb doc 2.8Mb extdata 1.5Mb

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘AlgDesign’ ‘GO.db’ ‘R.methodsS3’ ‘import’ ‘methods’ ‘org.Bt.eg.db’ ‘shinythemes’ All declared Imports should be used.

canceR

• Version: 1.30.01
• GitHub: https://github.com/kmezhoud/canceR
• Source code: https://github.com/cran/canceR
• Date/Publication: 2022-04-27
• Number of recursive dependencies: 169

Run revdep_details(, "canceR") for more info

In both

• checking whether package ‘canceR’ can be installed ... WARNING Found the following significant warnings: Warning: loading Rplot failed Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/R.oo/revdep/checks/canceR/new/canceR.Rcheck/00install.out’ for details.

• checking installed package size ... NOTE installed size is 19.6Mb sub-directories of 1Mb or more: doc 18.2Mb

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R.methodsS3’ All declared Imports should be used.

knitrProgressBar

• Version: 1.1.0
• GitHub: https://github.com/rmflight/knitrProgressBar
• Source code: https://github.com/cran/knitrProgressBar
• Date/Publication: 2018-02-20 04:04:54 UTC
• Number of recursive dependencies: 59

Run revdep_details(, "knitrProgressBar") for more info

In both

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

roxygen2

• Version: 7.2.0
• GitHub: https://github.com/r-lib/roxygen2
• Source code: https://github.com/cran/roxygen2
• Date/Publication: 2022-05-13 07:30:02 UTC
• Number of recursive dependencies: 62

Run revdep_details(, "roxygen2") for more info

In both

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

tmle.npvi

• Version: 0.10.0
• GitHub: NA
• Source code: https://github.com/cran/tmle.npvi
• Date/Publication: 2015-05-22 18:59:02
• Number of recursive dependencies: 41

Run revdep_details(, "tmle.npvi") for more info

In both

• checking R code for possible problems ... NOTE 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.

HenrikBengtsson/R.oo documentation built on Jan. 31, 2024, 9:06 a.m.