clusterExperiment 1.3.2
Elizabeth Purdom
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clusterExperiment | | Last Changed Rev: 130989 / Revision: 131943 | | Last Changed Date: 2017-07-05 19:50:37 -0400 (Wed, 05 Jul 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ ERROR ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && mkdir clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterExperiment.buildbin-libdir clusterExperiment_1.3.2.tar.gz >clusterExperiment.Rcheck\00install.out 2>&1 && cp clusterExperiment.Rcheck\00install.out clusterExperiment-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=clusterExperiment.buildbin-libdir --install="check:clusterExperiment-install.out" --force-multiarch --no-vignettes --timings clusterExperiment_1.3.2.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/clusterExperiment.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clusterExperiment/DESCRIPTION' ... OK
* this is package 'clusterExperiment' version '1.3.2'
* 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 'clusterExperiment' can be installed ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': 'ape:::.PlotPhyloEnv'
See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'ape:::.matchDataPhylo'
See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
mergeClusters.Rd: non-ASCII input and no declared encoding
plotClusters.Rd: non-ASCII input and no declared encoding
problems found in 'mergeClusters.Rd', 'plotClusters.Rd'
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
subsampleClustering 37.97 0.39 38.36
plotHeatmap 13.71 0.09 13.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
subsampleClustering 44.41 0.10 44.50
plotHeatmap 18.79 0.15 18.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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 ...Warning: running command '"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rcmd.exe" Rd2pdf --batch --no-preview --build-dir="C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSCX8xc/Rd2pdf2388bd36913" --no-clean -o clusterExperiment-manual.pdf "C:/Users/biocbuild/bbs-3.6-bioc/meat/clusterExperiment.buildbin-libdir/clusterExperiment"' had status 1
WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char  (U+9D)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
! Package inputenc Error: Unicode char  (U+9D)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
* checking PDF version of manual without hyperrefs or index ...Warning: running command '"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rcmd.exe" Rd2pdf --batch --no-preview --build-dir="C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSCX8xc/Rd2pdf2388338f58b8" --no-clean --no-index -o clusterExperiment-manual.pdf C:/Users/biocbuild/bbs-3.6-bioc/meat/clusterExperiment.buildbin-libdir/clusterExperiment' had status 1
ERROR
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/clusterExperiment.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'clusterExperiment' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'clusterExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterExperiment' as clusterExperiment_1.3.2.zip
* DONE (clusterExperiment)