Vanja Haberle
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/CAGEr |
| Branch: RELEASE_3_12 |
| Last Commit: 034e4bf |
| Last Changed Date: 2021-01-15 01:28:35 -0400 (Fri, 15 Jan 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:06 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the CAGEr package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 224/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CAGEr 1.32.1 (landing page) Vanja Haberle
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CAGEr |
| Version: 1.32.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAGEr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CAGEr_1.32.1.tar.gz |
| StartedAt: 2021-05-06 01:05:21 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:20:26 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 905.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CAGEr.Rcheck |
| Warnings: 4 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAGEr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CAGEr_1.32.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CAGEr.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '1.32.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CAGEr' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/CTSS-class.Rd:31: file link 'UnstitchedGPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/CTSS-class.Rd:34: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/CustomConsensusClusters.Rd:42: missing link '.ConsensusClusters'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/clusterCTSS.Rd:89: missing link 'TagClusters'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/consensusClusters.Rd:52: missing link 'ConsensusClusters'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/mapStats.Rd:29: file link 'mixedorder' in package 'gtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/tagClusters.Rd:58: missing link 'TagClusters'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CAGEr.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'CustomConsensusClusters.Rd':
'.ConsensusClusters'
Missing link or links in documentation object 'clusterCTSS.Rd':
'TagClusters'
Missing link or links in documentation object 'consensusClusters.Rd':
'ConsensusClusters'
Missing link or links in documentation object 'tagClusters.Rd':
'TagClusters'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'show' and siglist 'CTSS'
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 for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'CTSS-class'
'.Object' '...' 'bsgenomeName' 'seqnames' 'pos' 'strand' 'seqinfo'
'seqlengths' 'from' 'to' 'strict'
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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cumulativeCTSSdistribution 32.88 5.14 38.01
importPublicData 32.56 1.15 41.32
scoreShift 33.61 0.00 33.61
quantilePositions 23.39 0.57 23.99
aggregateTagClusters 14.84 0.01 14.86
clusterCTSS 11.11 0.44 11.55
consensusClusters 7.36 0.61 7.97
distclu-functions 6.56 0.69 7.25
CAGEexp-class 5.34 1.40 7.01
mergeCAGEsets 5.94 0.27 6.21
coverage-functions 5.25 0.31 5.57
strandInvaders 1.62 0.08 12.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cumulativeCTSSdistribution 30.41 5.45 35.86
scoreShift 34.76 0.00 34.76
importPublicData 28.78 1.33 34.69
quantilePositions 22.47 0.55 23.02
aggregateTagClusters 16.34 0.02 16.36
clusterCTSS 9.63 0.50 10.13
distclu-functions 6.14 0.80 6.94
consensusClusters 5.23 0.63 5.86
coverage-functions 5.05 0.58 5.63
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/CAGEr.Rcheck/00check.log'
for details.
CAGEr.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CAGEr_1.32.1.tar.gz && rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CAGEr.buildbin-libdir CAGEr_1.32.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CAGEr_1.32.1.zip && rm CAGEr_1.32.1.tar.gz CAGEr_1.32.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 768k 100 768k 0 0 36.0M 0 --:--:-- --:--:-- --:--:-- 37.5M
install for i386
* installing *source* package 'CAGEr' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CAGEr'
finding HTML links ... done
CAGEexp-class html
finding level-2 HTML links ... done
CAGEr-class html
CAGEr-package html
CAGEr_Multicore html
CAGEset-class html
CTSS-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/CTSS-class.Rd:31: file link 'UnstitchedGPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/CTSS-class.Rd:34: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
CTSSclusteringMethod html
CTSScoordinates html
CTSScumulativesTagClusters html
CTSSnormalizedTpm html
CTSStagCount html
CTSStagCountTable html
CTSStoGenes html
CustomConsensusClusters html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/CustomConsensusClusters.Rd:42: missing link '.ConsensusClusters'
FANTOM5humanSamples html
FANTOM5mouseSamples html
GeneExpDESeq2 html
GeneExpSE html
QuantileWidthFunctions html
aggregateTagClusters html
annotateCTSS html
bam2CTSS html
byCtss html
clusterAggregateAndSum html
clusterCTSS html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/clusterCTSS.Rd:89: missing link 'TagClusters'
coerceInBSgenome html
consensusClusterConvertors html
consensusClusters-set html
consensusClusters html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/consensusClusters.Rd:52: missing link 'ConsensusClusters'
consensusClustersDESeq2 html
consensusClustersQuantile html
consensusClustersTpm html
coverage-functions html
cumulativeCTSSdistribution html
distclu-functions html
exampleCAGEexp html
exampleCAGEset html
exampleZv9_annot html
exportCTSStoBedGraph html
exportToBed html
expressionClasses html
extractExpressionClass html
genomeName html
getCTSS html
getExpressionProfiles html
getShiftingPromoters html
hanabi-class html
hanabi html
hanabiPlot html
import.CAGEscanMolecule html
import.CTSS html
import.bam html
import.bam.ctss html
import.bedCTSS html
import.bedScore html
import.bedmolecule html
importPublicData html
inputFiles html
inputFilesType html
librarySizes html
loadFileIntoGPos html
mapStats html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/mapStats.Rd:29: file link 'mixedorder' in package 'gtools' does not exist and so has been treated as a topic
mapStatsScopes html
mergeCAGEsets html
mergeSamples html
moleculesGR2CTSS html
normalizeTagCount html
parseCAGEscanBlocksToGrangeTSS html
plot.hanabi html
plotAnnot html
plotCorrelation html
plotExpressionProfiles html
plotInterquantileWidth html
plotReverseCumulatives html
powerLaw html
quantilePositions html
ranges2annot html
ranges2genes html
ranges2names html
sampleLabels html
scoreShift html
seqNameTotalsSE html
setColors html
show-methods html
strandInvaders html
summariseChrExpr html
tagClusterConvertors html
tagClusters html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUBKecb/R.INSTALLe283b972f7e/CAGEr/man/tagClusters.Rd:58: missing link 'TagClusters'
tagClustersQuantile html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CAGEr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAGEr' as CAGEr_1.32.1.zip
* DONE (CAGEr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CAGEr' successfully unpacked and MD5 sums checked
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CAGEr.Rcheck/examples_i386/CAGEr-Ex.timings
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CAGEr.Rcheck/examples_x64/CAGEr-Ex.timings
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