|setting |value | |:--------|:----------------------------| |version |R version 3.4.0 (2017-04-21) | |system |x86_64, linux-gnu | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |tz |Zulu | |date |2017-06-17 |
|package |* |version |date |source | |:---------|:--|:---------|:----------|:----------------------------------| |BH | |1.62.0-1 |2016-11-19 |cran (@1.62.0-) | |DBI | |0.6-13 |2017-05-08 |Github (rstats-db/DBI@f6500a5) | |DBItest | |1.4-22 |2017-05-08 |Github (rstats-db/DBItest@1f344a3) | |knitr | |1.16 |2017-05-18 |cran (@1.16) | |memoise | |1.1.0 |2017-04-21 |CRAN (R 3.4.0) | |plogr | |0.1-1 |2016-09-24 |cran (@0.1-1) | |Rcpp | |0.12.11.2 |2017-06-05 |local | |rmarkdown | |1.6 |2017-06-15 |cran (@1.6) | |RSQLite | |1.1-17 |2017-06-17 |local | |testthat | |1.0.2 |2016-04-23 |cran (@1.0.2) |
32 packages with problems
|package |version | errors| warnings| notes| |:------------------|:--------|------:|--------:|-----:| |anchoredDistr |1.0.2 | 0| 1| 0| |AnnotationDbi |1.38.1 | 0| 1| 5| |AnnotationHubData |1.6.0 | 1| 0| 4| |BiocFileCache |1.0.0 | 1| 1| 0| |ChemmineR |2.28.0 | 1| 0| 0| |chunked |0.3 | 1| 0| 1| |clstutils |1.24.0 | 0| 2| 5| |CNEr |1.12.0 | 0| 2| 2| |etl |0.3.5 | 1| 1| 0| |GeneAnswers |2.18.0 | 1| 3| 6| |GenomicFeatures |1.28.3 | 0| 1| 3| |lumi |2.28.0 | 0| 2| 3| |maGUI |2.2 | 1| 0| 0| |metagenomeFeatures |1.8.0 | 1| 0| 0| |metaseqR |1.16.0 | 1| 1| 4| |mgsa |1.24.0 | 0| 1| 5| |MonetDBLite |0.3.1 | 2| 0| 3| |oce |0.9-21 | 1| 0| 1| |oligoClasses |1.38.0 | 0| 2| 4| |oligo |1.40.1 | 1| 1| 9| |Organism.dplyr |1.0.0 | 1| 0| 0| |PAnnBuilder |1.40.0 | 0| 3| 1| |plethy |1.14.0 | 2| 0| 3| |recoup |1.4.0 | 2| 0| 1| |RImmPort |1.4.1 | 0| 1| 0| |RQDA |0.2-8 | 1| 0| 1| |seqplots |1.13.0 | 2| 0| 3| |sqldf |0.4-10 | 0| 1| 2| |taxizedb |0.1.0 | 1| 0| 0| |TSdata |2016.8-1 | 0| 1| 0| |VariantFiltering |1.12.1 | 0| 1| 4| |vmsbase |2.1.3 | 1| 0| 0|
Maintainer: Heather Savoy frystacka@berkeley.edu
0 errors | 1 warning | 0 notes
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 50-64 (anchoredDistr.Rmd)
Error: processing vignette 'anchoredDistr.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Maintainer: Bioconductor Package Maintainer maintainer@bioconductor.org
0 errors | 1 warning | 5 notes
checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘org.testing.db’
checking installed package size ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
R 1.0Mb
extdata 6.0Mb
checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘utils’ ‘stats4’ ‘BiocGenerics’ ‘Biobase’ ‘IRanges’ ‘DBI’ ‘RSQLite’
A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘GO.db’ ‘KEGG.db’ ‘RSQLite’ ‘graph’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE
.selectInp8: no visible global function definition for ‘.resort’
annotMessage: no visible binding for global variable ‘pkgName’
createORGANISMSeeds: no visible global function definition for
‘makeAnnDbMapSeeds’
makeGOGraph: no visible binding for global variable ‘GOBPPARENTS’
makeGOGraph: no visible binding for global variable ‘GOMFPARENTS’
makeGOGraph: no visible binding for global variable ‘GOCCPARENTS’
makeGOGraph: no visible global function definition for ‘ftM2graphNEL’
Undefined global functions or variables:
.resort GOBPPARENTS GOCCPARENTS GOMFPARENTS ftM2graphNEL
makeAnnDbMapSeeds pkgName
checking Rd line widths ... NOTE
Rd file 'inpIDMapper.Rd':
\examples lines wider than 100 characters:
YeastUPSingles = inpIDMapper(ids, "HOMSA", "SACCE", destIDType="UNIPROT", keepMultDestIDMatches = FALSE)
These lines will be truncated in the PDF manual.
Maintainer: Bioconductor Package Maintainer maintainer@bioconductor.org
1 error | 0 warnings | 4 notes
checking tests ... ERROR
Running ‘AnnotationHubData_unit_tests.R’ [66s/149s]
Running the tests in ‘tests/AnnotationHubData_unit_tests.R’ failed.
Last 13 lines of output:
1 Test Suite :
AnnotationHubData RUnit Tests - 21 test functions, 1 error, 0 failures
ERROR in test_Grasp2Db_recipe: Error : object 'src_sql' is not exported by 'namespace:dplyr'
Test files with failing tests
test_recipe.R
test_Grasp2Db_recipe
Error in BiocGenerics:::testPackage("AnnotationHubData") :
unit tests failed for package AnnotationHubData
Execution halted
checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘BiocInstaller’
A package should be listed in only one of these fields.
checking top-level files ... NOTE
Non-standard file/directory found at top level:
‘appveyor.yml’
checking dependencies in R code ... NOTE
'library' or 'require' call to ‘BiocInstaller’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’
Unexported object imported by a ':::' call: ‘OrganismDbi:::.packageTaxIds’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
.NCBIMetadataFromUrl: no visible binding for global variable ‘results’
.NCBIMetadataFromUrl: no visible binding for global variable ‘specData’
.makeComplexGR: no visible binding for global variable ‘seqname’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Title’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Description’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘BiocVersion’
... 39 lines ...
test_Inparanoid8ImportPreparer_recipe: no visible binding for global
variable ‘BiocVersion’
test_Inparanoid8ImportPreparer_recipe: no visible global function
definition for ‘checkTrue’
trackWithAuxiliaryTablesToGRanges: no visible binding for global
variable ‘seqname’
Undefined global functions or variables:
BiocVersion Coordinate_1_based DataProvider Description DispatchClass
Genome Location_Prefix Maintainer RDataClass RDataDateAdded RDataPath
SourceType SourceUrl SourceVersion Species TaxonomyId Title ahroot
checkTrue results seqname specData suppresWarnings
Maintainer: Lori Shepherd lori.shepherd@roswellpark.org Bug reports: https://github.com/Bioconductor/BiocFileCache/issues
1 error | 1 warning | 0 notes
checking tests ... ERROR
Running ‘testthat.R’ [21s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
intersect, setdiff, setequal, union
>
> test_check("BiocFileCache")
1. Failure: bfcinfo works (@test_BiocFileCache_class.R#109) --------------------
bfcinfo(bfc) inherits from `tbl_bfc/tbl_dbi/tbl_sql/tbl_lazy/tbl` not `tbl_sqlite`.
testthat results ================================================================
OK: 116 SKIPPED: 0 FAILED: 1
1. Failure: bfcinfo works (@test_BiocFileCache_class.R#109)
Error: testthat unit tests failed
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
23: eval(expr, envir, enclos)
24: withVisible(eval(expr, envir, enclos))
25: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
26: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
27: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
28: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
... 8 lines ...
37: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
38: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv())
39: vweave_rmarkdown(...)
40: engine$weave(file, quiet = quiet, encoding = enc)
41: doTryCatch(return(expr), name, parentenv, handler)
42: tryCatchOne(expr, names, parentenv, handlers[[1L]])
43: tryCatchList(expr, classes, parentenv, handlers)
44: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA, call. = FALSE)})
45: buildVignettes(dir = "/home/muelleki/git/R/RSQLite/revdep/checks/BiocFileCache.Rcheck/vign_test/BiocFileCache")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
Maintainer: Thomas Girke thomas.girke@ucr.edu
1 error | 0 warnings | 0 notes
checking whether package ‘ChemmineR’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/ChemmineR.Rcheck/00install.out’ for details.
Maintainer: Edwin de Jonge edwindjonge@gmail.com Bug reports: https://github.com/edwindj/chunked/issues
1 error | 0 warnings | 1 note
checking tests ... ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1. Error: write_chunkwise to db works (@test-write.R#29) -----------------------
'sql_render' is not an exported object from 'namespace:dplyr'
1: write_chunkwise(iris2, tmp, row.names = FALSE) at testthat/test-write.R:29
2: write_chunkwise.tbl_sql(iris2, tmp, row.names = FALSE)
3: dplyr::sql_render
4: getExportedValue(pkg, name)
5: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)),
call. = FALSE, domain = NA)
testthat results ================================================================
OK: 28 SKIPPED: 0 FAILED: 1
1. Error: write_chunkwise to db works (@test-write.R#29)
Error: testthat unit tests failed
Execution halted
checking dependencies in R code ... NOTE
Missing or unexported object: ‘dplyr::sql_render’
Maintainer: Noah Hoffman ngh2@uw.edu
0 errors | 2 warnings | 5 notes
checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
tests/unit/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Loading required package: clst
Loading required package: rjson
Loading required package: ape
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'pplacerDemo.tex' failed.
LaTeX errors:
! Package auto-pst-pdf Error:
"shell escape" (or "write18") is not enabled:
auto-pst-pdf will not work!
.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
checking top-level files ... NOTE
Non-standard file/directory found at top level:
‘devmakefile’
checking dependencies in R code ... NOTE
'library' or 'require' call to ‘rjson’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' call to ‘RSVGTipsDevice’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘ape’ ‘rjson’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("seq_root2tip", ..., PACKAGE = "ape")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
checking R code for possible problems ... NOTE
edgeMap: no visible global function definition for ‘fromJSON’
findOutliers: no visible global function definition for ‘quantile’
findOutliers: no visible binding for global variable ‘median’
maxDists: no visible binding for global variable ‘median’
placeData: no visible global function definition for ‘read.table’
prettyTree: no visible binding for global variable ‘par’
prettyTree: no visible global function definition for ‘plot’
prettyTree: no visible binding for global variable ‘.PlotPhyloEnv’
prettyTree: no visible binding for global variable ‘points’
... 19 lines ...
taxonomyFromRefpkg: no visible global function definition for
‘read.csv’
Undefined global functions or variables:
.PlotPhyloEnv dev.off devSVGTips fromJSON legend median par plot
points quantile read.csv read.table setSVGShapeToolTip text
Consider adding
importFrom("grDevices", "dev.off")
importFrom("graphics", "legend", "par", "plot", "points", "text")
importFrom("stats", "median", "quantile")
importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
Maintainer: Ge Tan ge_tan@live.com Bug reports: https://github.com/ge11232002/CNEr/issues
0 errors | 2 warnings | 2 notes
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘addAncestorGO’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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 ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Object: ‘ucsc/pipeline.o’
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘ucsc/obscure.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Objects: ‘ucsc/axt.o’, ‘ucsc/errabort.o’, ‘ucsc/obscure.o’,
‘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’
File ‘CNEr/libs/CNEr.so’:
Found no call to: ‘R_useDynamicSymbols’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE
installed size is 29.4Mb
sub-directories of 1Mb or more:
R 11.5Mb
extdata 15.9Mb
libs 1.1Mb
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.
Maintainer: Ben Baumer ben.baumer@gmail.com Bug reports: https://github.com/beanumber/etl/issues
1 error | 1 warning | 0 notes
checking tests ... ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
downloaded 12 KB
trying URL 'http://www.nytimes.com'
Content type 'text/html; charset=utf-8' length 223051 bytes (217 KB)
==================================================
downloaded 217 KB
testthat results ================================================================
OK: 15 SKIPPED: 0 FAILED: 3
1. Error: sqlite works (@test-etl.R#9)
2. Failure: dplyr works (@test-etl.R#25)
3. Error: MonetDBLite works (@test-etl.R#54)
Error: testthat unit tests failed
Execution halted
checking Rd cross-references ... WARNING
Missing link or links in documentation object 'etl.Rd':
‘[dplyr]{src_sql}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Maintainer: Lei Huang lhuang7@uchicago.edu and Gang Feng gilbertfeng@gmail.com
1 error | 3 warnings | 6 notes
checking examples ... ERROR
Running examples in ‘GeneAnswers-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chartPlots
> ### Title: Pie Chart and Bar Plots
> ### Aliases: chartPlots
> ### Keywords: methods
>
> ### ** Examples
>
> x <- matrix(c(6,9,3,30,13,2,15,20), nrow = 4, ncol=2, byrow=FALSE,
+ dimnames = list(c("group1", "group2", "group3", "group4"),
+ c("value1", "value2")))
> chartPlots(x, chartType='all', specifiedCol = "value2", top = 3)
Error in x11() : screen devices should not be used in examples etc
Calls: chartPlots -> x11
Execution halted
checking whether package ‘GeneAnswers’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/GeneAnswers.Rcheck/00install.out’ for details.
checking sizes of PDF files under ‘inst/doc’ ... WARNING
‘gs+qpdf’ made some significant size reductions:
compacted ‘geneAnswers.pdf’ from 1374Kb to 600Kb
consider running tools::compactPDF(gs_quality = "ebook") on these files
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
Loading required package: org.Hs.eg.db
Loading required package: GO.db
Loading required package: KEGG.db
... 8 lines ...
Loading required package: org.Mm.eg.db
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'geneAnswers.tex' failed.
LaTeX errors:
! Package auto-pst-pdf Error:
"shell escape" (or "write18") is not enabled:
auto-pst-pdf will not work!
.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘igraph’ ‘RCurl’ ‘annotate’ ‘Biobase’ ‘XML’ ‘RSQLite’ ‘MASS’
‘Heatplus’ ‘RColorBrewer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking installed package size ... NOTE
installed size is 36.2Mb
sub-directories of 1Mb or more:
External 32.4Mb
data 1.1Mb
doc 1.6Mb
checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘annotate’
A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘Biobase’ ‘Heatplus’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘GO.db’ ‘KEGG.db’ ‘biomaRt’ ‘reactome.db’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE
Found an obsolete/platform-specific call in the following functions:
‘chartPlots’ ‘drawTable’
Found the platform-specific device:
‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
File ‘GeneAnswers/R/zzz.R’:
.onLoad calls:
require(Biobase)
... 78 lines ...
data("DmIALite", package = "GeneAnswers")
File ‘GeneAnswers/R/getDOLiteTerms.R’:
data("DOLiteTerm", package = "GeneAnswers")
File ‘GeneAnswers/R/zzz.R’:
data("DOLite", package = "GeneAnswers")
data("DOLiteTerm", package = "GeneAnswers")
data("HsIALite", package = "GeneAnswers")
data("MmIALite", package = "GeneAnswers")
data("RnIALite", package = "GeneAnswers")
data("DmIALite", package = "GeneAnswers")
See section ‘Good practice’ in ‘?data’.
checking Rd line widths ... NOTE
Rd file 'GeneAnswers-class.Rd':
\examples lines wider than 100 characters:
x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneEx ... [TRUNCATED]
Rd file 'GeneAnswers-package.Rd':
\examples lines wider than 100 characters:
x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneEx ... [TRUNCATED]
Rd file 'buildNet.Rd':
... 144 lines ...
## Not run: topDOLITEGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE)
Rd file 'topPATHGenes.Rd':
\examples lines wider than 100 characters:
## Not run: topPATHGenes(x, geneSymbol=TRUE, orderby='genenum', top=6, topGenes=8, genesOrderBy='foldChange')
Rd file 'topREACTOME.PATHGenes.Rd':
\examples lines wider than 100 characters:
## Not run: topREACTOME.PATHGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE)
These lines will be truncated in the PDF manual.
Maintainer: Bioconductor Package Maintainer maintainer@bioconductor.org
0 errors | 1 warning | 3 notes
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘exonicParts’ ‘intronicParts’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’
‘AnnotationDbi’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
‘rtracklayer:::resourceDescription’ ‘rtracklayer:::ucscTableOutputs’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
.writeMetadataFeatureTable: no visible global function definition for
‘packageDescription’
.writeMetadataTable: no visible global function definition for
‘packageDescription’
Undefined global functions or variables:
packageDescription
Consider adding
importFrom("utils", "packageDescription")
to your NAMESPACE file.
Maintainer: Pan Du dupan.mail@gmail.com, Lei Huang lhuang@bsd.uchicago.edu, Gang Feng g-feng@northwestern.edu
0 errors | 2 warnings | 3 notes
checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
‘IRanges’ ‘bigmemoryExtras’
checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘IlluminaAnnotation.R’, ‘IlluminaAnnotation.pdf’, ‘lumi.R’,
‘lumi.pdf’, ‘lumi_VST_evaluation.R’, ‘lumi_VST_evaluation.pdf’,
‘methylationAnalysis.R’, ‘methylationAnalysis.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
R 2.6Mb
data 3.6Mb
checking Rd line widths ... NOTE
Rd file 'IlluminaID2nuID.Rd':
\usage lines wider than 90 characters:
IlluminaID2nuID(IlluminaID, lib.mapping=NULL, species = c("Human", "Mouse", "Rat", "Unknown"), chipVersion = NULL, ...)
Rd file 'addAnnotationInfo.Rd':
\usage lines wider than 90 characters:
addAnnotationInfo(methyLumiM, lib = 'FDb.InfiniumMethylation.hg19', annotationColumn=c('COLOR_CHANNEL', 'CHROMOSOME', 'POSITION'))
Rd file 'addNuID2lumi.Rd':
... 177 lines ...
smoothQuantileNormalization(dataMatrix, ref = NULL, adjData=NULL, logMode = TRUE, bandwidth = NULL, degree = 1, verbose = FALSE, ...)
Rd file 'ssn.Rd':
\usage lines wider than 90 characters:
ssn(x.lumi, targetArray = NULL, scaling = TRUE, bgMethod=c('density', 'mean', 'median', 'none'), fgMethod=c('mean', 'density', 'median' ... [TRUNCATED]
Rd file 'vst.Rd':
\usage lines wider than 90 characters:
vst(u, std, nSupport = min(length(u), 500), backgroundStd=NULL, fitMethod = c('linear', 'quadratic'), lowCutoff = 1/3, ifPlot = FALSE)
These lines will be truncated in the PDF manual.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘bigmemoryExtras’
Maintainer: Dhammapal Bharne dhammapalb@uohyd.ac.in
1 error | 0 warnings | 0 notes
checking whether package ‘maGUI’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/maGUI.Rcheck/00install.out’ for details.
Maintainer: Nathan D. Olson nolson@umiacs.umd.edu Bug reports: https://github.com/HCBravoLab/metagenomeFeatures/issues
1 error | 0 warnings | 0 notes
checking whether package ‘metagenomeFeatures’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/metagenomeFeatures.Rcheck/00install.out’ for details.
Maintainer: Panagiotis Moulos moulos@fleming.gr
1 error | 1 warning | 4 notes
checking tests ... ERROR
Running ‘runTests.R’ [21s/23s]
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
ERROR in test_estimate_aufc_weights: Error in .check_ncores(cores) : 7 simultaneous processes spawned
ERROR in test_metaseqr: Error in .check_ncores(cores) : 5 simultaneous processes spawned
Test files with failing tests
test_estimate_aufc_weights.R
test_estimate_aufc_weights
test_metaseqr.R
test_metaseqr
Error in BiocGenerics:::testPackage("metaseqR") :
unit tests failed for package metaseqR
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
The following objects are masked from 'package:ShortRead':
left, right
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
... 8 lines ...
plotMA
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: qvalue
Quitting from lines 119-159 (metaseqr-pdf.Rnw)
Error: processing vignette 'metaseqr-pdf.Rnw' failed with diagnostics:
7 simultaneous processes spawned
Execution halted
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘TCC’
checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘BSgenome’ ‘BiocInstaller’ ‘GenomicRanges’ ‘RMySQL’ ‘RSQLite’
‘Rsamtools’ ‘TCC’ ‘VennDiagram’ ‘parallel’ ‘rtracklayer’ ‘survcomp’
‘zoo’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE
biasPlotToJSON: no visible binding for global variable ‘nams’
cddat: no visible global function definition for ‘assayData’
cddat: no visible global function definition for ‘ks.test’
cddat: no visible global function definition for ‘p.adjust’
cdplot: no visible global function definition for ‘plot’
cdplot: no visible global function definition for ‘lines’
countsBioToJSON: no visible binding for global variable ‘nams’
diagplot.avg.ftd : <anonymous>: no visible binding for global variable
‘sd’
... 246 lines ...
"dev.off", "jpeg", "pdf", "png", "postscript", "tiff")
importFrom("graphics", "abline", "arrows", "axis", "grid", "lines",
"mtext", "par", "plot", "plot.new", "plot.window", "points",
"text", "title")
importFrom("methods", "as", "new")
importFrom("stats", "as.dist", "cmdscale", "cor", "end", "ks.test",
"mad", "median", "model.matrix", "na.exclude", "optimize",
"p.adjust", "p.adjust.methods", "pchisq", "quantile",
"rexp", "rnbinom", "runif", "sd", "start", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Maintainer: Sebastian Bauer mail@sebastianbauer.info
0 errors | 1 warning | 5 notes
checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
checking top-level files ... NOTE
Non-standard files/directories found at top level:
‘acinclude.m4’ ‘aclocal.m4’ ‘script’
checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘mgsa’ 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
'library' or 'require' call to ‘gplots’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘DBI’ ‘GO.db’ ‘RSQLite’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘gplots’ ‘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
createMgsaGoSets: no visible global function definition for ‘new’
mcmcSummary: no visible binding for global variable ‘sd’
mgsa.wrapper: no visible global function definition for ‘str’
mgsa.wrapper: no visible global function definition for ‘new’
readGAF: no visible global function definition for ‘read.delim’
readGAF: no visible global function definition for ‘na.omit’
readGAF: no visible global function definition for ‘new’
initialize,MgsaSets: no visible global function definition for
‘callNextMethod’
... 10 lines ...
‘close.screen’
Undefined global functions or variables:
barplot2 callNextMethod close.screen na.omit new par read.delim
relist screen sd split.screen str
Consider adding
importFrom("graphics", "close.screen", "par", "screen", "split.screen")
importFrom("methods", "callNextMethod", "new")
importFrom("stats", "na.omit", "sd")
importFrom("utils", "read.delim", "relist", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
checking compiled code ... NOTE
File ‘mgsa/libs/mgsa.so’:
Found no call to: ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Maintainer: Hannes Muehleisen hannes@cwi.nl Bug reports: https://github.com/hannesmuehleisen/MonetDBLite/issues
2 errors | 0 warnings | 3 notes
checking examples ... ERROR
Running examples in ‘MonetDBLite-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: src_monetdb
> ### Title: dplyr integration from MonetDBLite
> ### Aliases: src_monetdb src_monetdblite tbl.src_monetdb
> ### src_desc.src_monetdb src_translate_env.src_monetdb
> ### sample_frac.tbl_monetdb sample_n.tbl_monetdb
... 18 lines ...
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> # Connection basics ---------------------------------------------------------
> # To connect to a database first create a src:
> dbdir <- file.path(tempdir(), "dplyrdir")
> my_db <- MonetDBLite::src_monetdb(embedded=dbdir)
Error: 'src_sql' is not an exported object from 'namespace:dplyr'
Execution halted
checking tests ... ERROR
Running ‘testthat.R’ [18s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
testthat results ================================================================
OK: 132 SKIPPED: 0 FAILED: 13
1. Error: we can connect (@test_03_dplyr.R#15)
2. Error: dplyr copy_to() (@test_03_dplyr.R#27)
3. Error: dplyr tbl( sql() ) (@test_03_dplyr.R#35)
4. Error: dplyr select() (@test_03_dplyr.R#43)
5. Error: dplyr filter() (@test_03_dplyr.R#51)
6. Error: dplyr arrange() (@test_03_dplyr.R#59)
7. Error: dplyr mutate() (@test_03_dplyr.R#67)
8. Error: dplyr summarise() (@test_03_dplyr.R#75)
9. Error: dplyr multiple objects (@test_03_dplyr.R#84)
1. ...
Error: testthat unit tests failed
Execution halted
checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 6.6Mb
checking dependencies in R code ... NOTE
Missing or unexported objects:
‘dplyr::base_agg’ ‘dplyr::base_scalar’ ‘dplyr::base_win’
‘dplyr::build_sql’ ‘dplyr::is.ident’ ‘dplyr::sql_infix’
‘dplyr::sql_prefix’ ‘dplyr::sql_translator’ ‘dplyr::sql_variant’
‘dplyr::src_sql’ ‘dplyr::tbl_sql’
checking compiled code ... NOTE
File ‘MonetDBLite/libs/libmonetdb5.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Maintainer: Dan Kelley Dan.Kelley@Dal.Ca Bug reports: https://github.com/dankelley/oce/issues
1 error | 0 warnings | 1 note
checking examples ... ERROR
Running examples in ‘oce-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.oce
> ### Title: Read an Oceanographic Data File
> ### Aliases: read.oce
>
> ### ** Examples
>
>
> library(oce)
> x <- read.oce(system.file("extdata", "ctd.cnv", package="oce"))
> plot(x) # summary with TS and profiles
Error in if (!is.null(x@metadata$startTime) && 4 < nchar(x@metadata$startTime, :
missing value where TRUE/FALSE needed
Calls: plot -> plot -> .local
Execution halted
checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
help 2.1Mb
Maintainer: Benilton Carvalho beniltoncarvalho@gmail.com and Robert Scharpf rscharpf@jhsph.edu
0 errors | 2 warnings | 4 notes
checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'CNSet,ANY,ANY,ANY'
generic '[' and siglist 'gSetList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘scriptsForExampleData/CreateExampleData.R’
Package has no Sweave vignette sources and no VignetteBuilder field.
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doRedis’
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
getSequenceLengths: no visible binding for global variable ‘seqlengths’
pdPkgFromBioC: no visible binding for global variable ‘contrib.url’
pdPkgFromBioC: no visible global function definition for
‘available.packages’
pdPkgFromBioC: no visible global function definition for
‘install.packages’
chromosome,gSetList: no visible global function definition for
‘chromosomeList’
coerce,CNSet-CopyNumberSet: no visible global function definition for
‘totalCopynumber’
geometry,FeatureSet: no visible global function definition for ‘getPD’
Undefined global functions or variables:
available.packages chromosomeList contrib.url getPD install.packages
seqlengths totalCopynumber
Consider adding
importFrom("utils", "available.packages", "contrib.url",
"install.packages")
to your NAMESPACE file.
checking Rd line widths ... NOTE
Rd file 'AssayDataList.Rd':
\examples lines wider than 100 characters:
r <- lapply(r, function(x,dns) {dimnames(x) <- dns; return(x)}, dns=list(letters[1:5], LETTERS[1:5]))
Rd file 'GenomeAnnotatedDataFrameFrom-methods.Rd':
\examples lines wider than 100 characters:
dimnames=list(c("rs10000092","rs1000055", "rs100016", "rs10003241", "rs10004197"), NULL))
Rd file 'largeObjects.Rd':
\usage lines wider than 90 characters:
initializeBigMatrix(name=basename(tempfile()), nr=0L, nc=0L, vmode = "integer", initdata = NA)
Rd file 'oligoSetExample.Rd':
\examples lines wider than 100 characters:
copyNumber=integerMatrix(log2(locusLevelData[["copynumber"]]/100), 100),
These lines will be truncated in the PDF manual.
Maintainer: Benilton Carvalho benilton@unicamp.br
1 error | 1 warning | 9 notes
checking examples ... ERROR
Running examples in ‘oligo-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MAplot
> ### Title: MA plots
> ### Aliases: MAplot MAplot-methods MAplot,FeatureSet-method
> ### MAplot,TilingFeatureSet-method MAplot,PLMset-method
> ### MAplot,ExpressionSet-method MAplot,matrix-method
... 8 lines ...
+ groups <- factor(rep(c('brain', 'UnivRef'), each=3))
+ data.frame(sampleNames(nimbleExpressionFS), groups)
+ MAplot(nimbleExpressionFS, pairs=TRUE, ylim=c(-.5, .5), groups=groups)
+ }
Loading required package: oligoData
Loading required package: pd.hg18.60mer.expr
Loading required package: RSQLite
Loading required package: DBI
Error in loadNamespace(name) : there is no package called ‘KernSmooth’
Calls: MAplot ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
‘Makefile’
checking installed package size ... NOTE
installed size is 30.2Mb
sub-directories of 1Mb or more:
R 1.1Mb
doc 12.9Mb
scripts 15.7Mb
checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘biomaRt’ ‘AnnotationDbi’ ‘GenomeGraphs’ ‘RCurl’ ‘ff’
A package should be listed in only one of these fields.
checking top-level files ... NOTE
Non-standard file/directory found at top level:
‘TODO.org’
checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘oligo’ 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
Unexported object imported by a ':::' call: ‘Biobase:::annotatedDataFrameFromMatrix’
See the note in ?`:::` about the use of this operator.
checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("ReadHeader", ..., PACKAGE = "affyio")
.Call("read_abatch", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
checking R code for possible problems ... NOTE
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
partial argument match of 'nr' to 'nrow'
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
partial argument match of 'nc' to 'ncol'
NUSE: no visible global function definition for ‘abline’
RLE: no visible global function definition for ‘abline’
basicMvApairsPlot: no visible binding for global variable
‘smoothScatter’
basicMvApairsPlot: no visible global function definition for ‘frame’
... 36 lines ...
Undefined global functions or variables:
IQR abline aggregate approx complete.cases data frame intensities
loess man_fsetid mtext predict rnorm smooth.spline smoothScatter
splinefun text
Consider adding
importFrom("graphics", "abline", "frame", "mtext", "smoothScatter",
"text")
importFrom("stats", "IQR", "aggregate", "approx", "complete.cases",
"loess", "predict", "rnorm", "smooth.spline", "splinefun")
importFrom("utils", "data")
to your NAMESPACE file.
checking Rd line widths ... NOTE
Rd file 'basicRMA.Rd':
\usage lines wider than 90 characters:
basicRMA(pmMat, pnVec, normalize = TRUE, background = TRUE, bgversion = 2, destructive = FALSE, verbose = TRUE, ...)
Rd file 'fitProbeLevelModel.Rd':
\usage lines wider than 90 characters:
fitProbeLevelModel(object, background=TRUE, normalize=TRUE, target="core", method="plm", verbose=TRUE, S4=TRUE, ...)
Rd file 'getProbeInfo.Rd':
\usage lines wider than 90 characters:
getProbeInfo(object, field, probeType = "pm", target = "core", sortBy = c("fid", "man_fsetid", "none"), ...)
\examples lines wider than 100 characters:
agenGene <- getProbeInfo(affyGeneFS, field=c('fid', 'fsetid', 'type'), target='probeset', subset= type == 'control->bgp->antigenomic ... [TRUNCATED]
Rd file 'preprocessTools.Rd':
\usage lines wider than 90 characters:
backgroundCorrect(object, method=backgroundCorrectionMethods(), copy=TRUE, extra, subset=NULL, target='core', verbose=TRUE)
normalize(object, method=normalizationMethods(), copy=TRUE, subset=NULL,target='core', verbose=TRUE, ...)
These lines will be truncated in the PDF manual.
checking compiled code ... NOTE
File ‘oligo/libs/oligo.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Maintainer: Martin Morgan martin.morgan@roswellpark.org
1 error | 0 warnings | 0 notes
checking whether package ‘Organism.dplyr’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/Organism.dplyr.Rcheck/00install.out’ for details.
Maintainer: Li Hong sysptm@gmail.com
0 errors | 3 warnings | 1 note
checking dependencies in R code ... WARNING
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
Please remove these calls from your code.
':::' calls which should be '::':
‘AnnotationDbi:::as.list’ ‘base:::get’ ‘tools:::list_files_with_type’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::createAnnDbBimaps’
‘AnnotationDbi:::prefixAnnObjNames’ ‘tools:::makeLazyLoadDB’
See the note in ?`:::` about the use of this operator.
Including base/recommended package(s):
‘tools’
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘getShortSciName’ ‘twoStepSplit’
checking R code for possible problems ... WARNING
Found an obsolete/platform-specific call in the following function:
‘makeLLDB’
Found the defunct/removed function:
‘.saveRDS’
In addition to the above warning(s), found the following notes:
File ‘PAnnBuilder/R/zzz.R’:
.onLoad calls:
require(Biobase)
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
Found the following calls to data() loading into the global environment:
File ‘PAnnBuilder/R/writeManPage.R’:
data("descriptionInfo")
data("descriptionInfo")
See section ‘Good practice’ in ‘?data’.
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
}
trying URL 'http://gpcr2.biocomp.unibo.it/bacello/dataset.htm'
Content type 'text/html; charset=iso-8859-1' length 5062 bytes
==================================================
downloaded 5062 bytes
... 8 lines ...
Warning in rsqlite_disconnect(conn@ptr) :
There are 1 result in use. The connection will be released when they are closed
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'PAnnBuilder.tex' failed.
LaTeX errors:
! Package auto-pst-pdf Error:
"shell escape" (or "write18") is not enabled:
auto-pst-pdf will not work!
.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘utils’ ‘Biobase’ ‘RSQLite’ ‘AnnotationDbi’
A package should be listed in only one of these fields.
Maintainer: Daniel Bottomly bottomly@ohsu.edu
2 errors | 0 warnings | 3 notes
checking examples ... ERROR
Running examples in ‘plethy-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Utility functions
> ### Title: Utility functions to assist with QA/QC and analysis of
> ### plethysmography data
> ### Aliases: add.labels.by.sample get.err.breaks adjust.labels proc.sanity
> ### Keywords: Utilities
... 21 lines ...
> temp.db.file <- tempfile()
> write(sim.bux.lines, file=temp.file)
> test.bux.db <- parse.buxco(file.name=temp.file, db.name=temp.db.file, chunk.size=10000)
Processing /tmp/RtmpnYsv1v/filecd4029341423 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Error in if (sum(which.gt) > 0) { : missing value where TRUE/FALSE needed
Calls: parse.buxco ... write.sample.breaks -> write.sample.db -> sanity.check.time
Execution halted
checking tests ... ERROR
Running ‘runTests.R’ [25s/25s]
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
Test files with failing tests
test_check_helpers.R
test.add.labels.by.sample
test.dbImport
test.get.err.breaks
test.summaryMeasures
Error in BiocGenerics:::testPackage("plethy") :
unit tests failed for package plethy
In addition: Warning message:
In .Internal(gc(verbose, reset)) :
closing unused connection 3 (/tmp/RtmpI3SlBZ/filecdcd719faa07)
Execution halted
checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’
checking R code for possible problems ... NOTE
generate.sample.buxco : <anonymous> : <anonymous> : <anonymous> :
<anonymous>: no visible global function definition for ‘rnorm’
make.db.package: no visible global function definition for
‘packageDescription’
mvtsplot.data.frame: no visible global function definition for ‘colors’
mvtsplot.data.frame: no visible global function definition for ‘par’
mvtsplot.data.frame: no visible global function definition for ‘layout’
mvtsplot.data.frame: no visible global function definition for
‘strwidth’
... 14 lines ...
tsplot,BuxcoDB: no visible binding for global variable ‘Sample_Name’
Undefined global functions or variables:
Axis Days Sample_Name Value abline bxp colors layout legend lines
median mtext packageDescription par plot rnorm strwidth terms
Consider adding
importFrom("grDevices", "colors")
importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend",
"lines", "mtext", "par", "plot", "strwidth")
importFrom("stats", "median", "rnorm", "terms")
importFrom("utils", "packageDescription")
to your NAMESPACE file.
checking Rd line widths ... NOTE
Rd file 'parsing.Rd':
\usage lines wider than 90 characters:
parse.buxco(file.name = NULL, table.delim = "Table", burn.in.lines = c("Measurement", "Create measurement", "Waiting for", "Site Acknow ... [TRUNCATED]
chunk.size = 500, db.name = "bux_test.db", max.run.time.minutes = 60, overwrite = TRUE, verbose=TRUE, make.package = F, author = NULL ... [TRUNCATED]
parse.buxco.basic(file.name=NULL, table.delim="Table", burn.in.lines=c("Measurement", "Create measurement", "Waiting for", "Site Acknow ... [TRUNCATED]
Rd file 'utilities.Rd':
\usage lines wider than 90 characters:
get.err.breaks(bux.db, max.exp.count=150, max.acc.count=900, vary.perc=.1, label.val="ERR")
proc.sanity(bux.db, max.exp.time=300, max.acc.time=1800, max.exp.count=150, max.acc.count=900)
\examples lines wider than 100 characters:
err.dta <- data.frame(samples=samples, count=count, measure_break=measure_break, table_break=table_break, phase=phase, stringsAsFactors ... [TRUNCATED]
sample.labels <- data.frame(samples=c("sample_1","sample_3"), response_type=c("high", "low"),stringsAsFactors=FALSE)
These lines will be truncated in the PDF manual.
Maintainer: Panagiotis Moulos moulos@fleming.gr
2 errors | 0 warnings | 1 note
checking examples ... ERROR
Running examples in ‘recoup-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kmeansDesign
> ### Title: Apply k-means clustering to profile data
> ### Aliases: kmeansDesign
>
> ### ** Examples
... 16 lines ...
+ rc=0.5
+ )
Getting main ranges for measurements
measurement type: chipseq
genomic region type: tss
Calculating requested regions coverage for WT H4K20me1
processing chr12
Error in .check_ncores(cores) : 4 simultaneous processes spawned
Calls: recoup ... lapply -> FUN -> cmclapply -> mclapply -> .check_ncores
Execution halted
** found \donttest examples: check also with --run-donttest
checking tests ... ERROR
Running ‘runTests.R’ [15s/16s]
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
1 Test Suite :
recoup RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test_recoup: Error in .check_ncores(cores) : 4 simultaneous processes spawned
Test files with failing tests
test_recoup.R
test_recoup
Error in BiocGenerics:::testPackage("recoup") :
unit tests failed for package recoup
Execution halted
checking R code for possible problems ... NOTE
baseCoverageMatrix: no visible global function definition for
‘runValue’
baseCoverageMatrix : <anonymous>: no visible global function definition
for ‘runValue’
binCoverageMatrix : <anonymous>: no visible global function definition
for ‘runValue’
buildAnnotationStore: no visible global function definition for
‘Seqinfo’
calcCoverage: no visible global function definition for ‘runValue’
... 66 lines ...
recoupProfile: no visible binding for global variable ‘Design’
reduceExons : <anonymous>: no visible global function definition for
‘DataFrame’
splitVector: no visible global function definition for ‘Rle’
Undefined global functions or variables:
Condition Coverage DataFrame Design IRanges Index Rle ScanBamParam
Seqinfo Signal alphabetFrequency bamWhich<- biocLite dbConnect
dbDisconnect dbDriver dbGetQuery dbWriteTable flankedSexon gene
genomeRanges getBSgenome grid.text indexBam installed.genomes
mclapply mcmapply runValue seqlevels seqlevels<- sexon sortBam
subjectHits
Maintainer: Ravi Shankar rshankar@stanford.edu
0 errors | 1 warning | 0 notes
checking sizes of PDF files under ‘inst/doc’ ... WARNING
‘gs+qpdf’ made some significant size reductions:
compacted ‘RImmPort_Article.pdf’ from 735Kb to 339Kb
consider running tools::compactPDF(gs_quality = "ebook") on these files
Maintainer: HUANG Ronggui ronggui.huang@gmail.com
1 error | 0 warnings | 1 note
checking whether package ‘RQDA’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/RQDA.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rjpod’
Maintainer: Przemyslaw Stempor ps562@cam.ac.uk Bug reports: http://github.com/przemol/seqplots/issues
2 errors | 0 warnings | 3 notes
checking examples ... ERROR
Running examples in ‘seqplots-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotAverage
> ### Title: Create the average plot
> ### Aliases: plotAverage plotAverage,PlotSetArray-method
> ### plotAverage,PlotSetList-method plotAverage,PlotSetPair-method
> ### plotAverage,list-method
... 21 lines ...
> if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
+ plotset1 <- getPlotSetArray(bw1, c(bed1, bed2), 'ce10')
+ } else {
+ load(system.file("extdata", "precalc_plotset.Rdata", package="seqplots"))
+ }
character
Processing: Transcripts_ce10_chrI_100Kb.bed @ GSM1208360_chrI_100Kb_q5_sample.bw [ 1 / 2 ]
Error in close.connection(file) : invalid connection
Calls: getPlotSetArray ... lapply -> lapply -> FUN -> close -> close.connection
Execution halted
** found \donttest examples: check also with --run-donttest
checking tests ... ERROR
Running ‘test-all.R’ [24s/24s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
Error in signalCondition(e) :
no function to return from, jumping to top level
Calls: <Anonymous> ... close.connection -> .handleSimpleError -> h -> signalCondition
testthat results ================================================================
OK: 63 SKIPPED: 0 FAILED: 7
1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#21)
2. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#21)
3. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53)
4. Error: Test motifs (@test1.R#106)
5. Error: Test motifs (@test1.R#106)
6. Error: Test motifs (@test1.R#137)
7. Error: Test motifs (@test1.R#137)
Error: testthat unit tests failed
Execution halted
checking installed package size ... NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
R 1.1Mb
doc 2.4Mb
seqplots 4.9Mb
checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("BWGFile_summary", ..., PACKAGE = "rtracklayer")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
checking R code for possible problems ... NOTE
getPlotSetArray : <anonymous>: no visible global function definition
for ‘qt’
getSF : <anonymous>: no visible global function definition for ‘approx’
ggHeatmapPlotWrapper: no visible global function definition for
‘colorRampPalette’
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var2’
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var1’
ggHeatmapPlotWrapper: no visible binding for global variable ‘value’
heatmapPlotWrapper: no visible global function definition for
... 42 lines ...
capture.output colorRampPalette cutree dist hclust image kmeans
layout lines mtext par plot.new qt rainbow rect rgb title value
Consider adding
importFrom("grDevices", "adjustcolor", "colorRampPalette", "rainbow",
"rgb")
importFrom("graphics", "abline", "axis", "box", "image", "layout",
"lines", "mtext", "par", "plot.new", "rect", "title")
importFrom("stats", "approx", "as.dendrogram", "cutree", "dist",
"hclust", "kmeans", "qt")
importFrom("utils", "capture.output")
to your NAMESPACE file.
Maintainer: G. Grothendieck ggrothendieck@gmail.com Bug reports: http://groups.google.com/group/sqldf
0 errors | 1 warning | 2 notes
checking whether package ‘sqldf’ can be installed ... WARNING
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/sqldf.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE
'library' or 'require' call to ‘tcltk’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE
read.csv.sql: no visible global function definition for ‘download.file’
sqldf: no visible global function definition for ‘modifyList’
sqldf: no visible global function definition for ‘head’
Undefined global functions or variables:
download.file head modifyList
Consider adding
importFrom("utils", "download.file", "head", "modifyList")
to your NAMESPACE file.
Maintainer: Scott Chamberlain myrmecocystus+r@gmail.com Bug reports: https://github.com/ropensci/taxizedb/issues
1 error | 0 warnings | 0 notes
checking tests ... ERROR
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("taxizedb")
Loading required package: taxizedb
1. Failure: sql_collect works (@test-sql_collect.R#9) --------------------------
`src` inherits from `src_dbi/src_sql/src` not `src_sqlite`.
testthat results ================================================================
OK: 34 SKIPPED: 4 FAILED: 1
1. Failure: sql_collect works (@test-sql_collect.R#9)
Error: testthat unit tests failed
Execution halted
Maintainer: Paul Gilbert pgilbert.ttv9z@ncf.ca
0 errors | 1 warning | 0 notes
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetData/QNA/CAN+USA+MEX.B1_GE.CARSA.Q?format=compact_v2
Jun 17, 2017 5:58:48 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest
Jun 17, 2017 5:58:48 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest
Jun 17, 2017 5:58:48 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/datastructure/ESTAT/DSD_ei_nama_q/1.0
... 8 lines ...
INFO: The sdmx call returned messages in the footer:
Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]
Jun 17, 2017 5:58:49 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]
Error: processing vignette 'Guide.Stex' failed with diagnostics:
chunk 5
Error in .local(serIDs, con, ...) :
ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxXmlContentException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider.
Execution halted
Maintainer: Robert Castelo robert.castelo@upf.edu Bug reports: https://github.com/rcastelo/VariantFiltering/issues
0 errors | 1 warning | 4 notes
checking sizes of PDF files under ‘inst/doc’ ... WARNING
‘gs+qpdf’ made some significant size reductions:
compacted ‘usingVariantFiltering.pdf’ from 415Kb to 154Kb
consider running tools::compactPDF(gs_quality = "ebook") on these files
checking installed package size ... NOTE
installed size is 8.0Mb
sub-directories of 1Mb or more:
R 3.7Mb
extdata 3.5Mb
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'S4Vectors:::labeledLine' 'VariantAnnotation:::.checkArgs'
'VariantAnnotation:::.consolidateHits'
'VariantAnnotation:::.returnEmpty'
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:
'.adjustForStrandSense'
checking Rd line widths ... NOTE
Rd file 'MafDb-class.Rd':
\examples lines wider than 100 characters:
## founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression.
Rd file 'MafDb2-class.Rd':
\examples lines wider than 100 characters:
## founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression.
Rd file 'VariantFilteringParam-class.Rd':
... 19 lines ...
Rd file 'autosomalRecessiveHeterozygous.Rd':
\usage lines wider than 90 characters:
BPPARAM=bpparam("SerialParam"))
Rd file 'autosomalRecessiveHomozygous.Rd':
\usage lines wider than 90 characters:
use=c("everything", "complete.obs", "all.obs"),
BPPARAM=bpparam("SerialParam"))
These lines will be truncated in the PDF manual.
checking compiled code ... NOTE
File ‘VariantFiltering/libs/VariantFiltering.so’:
Found no call to: ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Maintainer: Lorenzo D'Andrea support@vmsbase.org
1 error | 0 warnings | 0 notes
checking whether package ‘vmsbase’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/vmsbase.Rcheck/00install.out’ for details.
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