Meena Choi
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/MSstats |
| Branch: RELEASE_3_6 |
| Last Commit: d6af3ee |
| Last Changed Date: 2018-02-12 17:00:35 -0400 (Mon, 12 Feb 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:23:27 -0400 (Thu, 12 Apr 2018).
| Package 906/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSstats 3.10.6 Meena Choi
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: MSstats |
| Version: 3.10.6 |
| Command: rm -rf MSstats.buildbin-libdir MSstats.Rcheck && mkdir MSstats.buildbin-libdir MSstats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSstats.buildbin-libdir MSstats_3.10.6.tar.gz >MSstats.Rcheck\00install.out 2>&1 && cp MSstats.Rcheck\00install.out MSstats-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MSstats.buildbin-libdir --install="check:MSstats-install.out" --force-multiarch --no-vignettes --timings MSstats_3.10.6.tar.gz |
| StartedAt: 2018-04-12 01:40:20 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:47:36 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 436.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSstats.Rcheck |
| Warnings: 1 |
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### Running command:
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### rm -rf MSstats.buildbin-libdir MSstats.Rcheck && mkdir MSstats.buildbin-libdir MSstats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSstats.buildbin-libdir MSstats_3.10.6.tar.gz >MSstats.Rcheck\00install.out 2>&1 && cp MSstats.Rcheck\00install.out MSstats-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MSstats.buildbin-libdir --install="check:MSstats-install.out" --force-multiarch --no-vignettes --timings MSstats_3.10.6.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MSstats.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSstats/DESCRIPTION' ... OK
* this is package 'MSstats' version '3.10.6'
* 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 'MSstats' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXA2AK/R.INSTALL35cc1ad33f29/MSstats/man/transformMSnSetToMSstats.Rd:26: missing file link 'MSnSet'
Warning: replacing previous import 'foreach::accumulate' by 'purrr::accumulate' when loading 'MSstats'
Warning: replacing previous import 'foreach::when' by 'purrr::when' when loading 'MSstats'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MSstats.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
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.iter.wls.fit.model: no visible binding for global variable 'weight'
.multiplot: no visible global function definition for 'grid.newpage'
.multiplot: no visible global function definition for 'pushViewport'
.multiplot: no visible global function definition for 'grid.layout'
.runQuantification: no visible binding for global variable
'datafeature'
DIAUmpiretoMSstatsFormat: no visible binding for global variable
'Selected_fragments'
DIAUmpiretoMSstatsFormat: no visible binding for global variable
'Selected_peptides'
DIAUmpiretoMSstatsFormat: no visible binding for global variable 'fea'
DIAUmpiretoMSstatsFormat: no visible binding for global variable
'Intensity'
OpenSWATHtoMSstatsFormat: no visible binding for global variable
'missing.col'
OpenSWATHtoMSstatsFormat: no visible binding for global variable
'aggr_Fragment_Annotation'
OpenSWATHtoMSstatsFormat: no visible binding for global variable
'aggr_Peak_Area'
OpenSWATHtoMSstatsFormat: no visible binding for global variable 'fea'
OpenSWATHtoMSstatsFormat: no visible binding for global variable
'Intensity'
OpenSWATHtoMSstatsFormat: no visible binding for global variable
'PeptideSequence'
OpenSWATHtoMSstatsFormat: no visible binding for global variable
'ProteinName'
SkylinetoMSstatsFormat: no visible binding for global variable
'PeptideSequence'
SkylinetoMSstatsFormat: no visible binding for global variable
'ProteinName'
SkylinetoMSstatsFormat: no visible binding for global variable 'fea'
SkylinetoMSstatsFormat: no visible binding for global variable
'Intensity'
SpectronauttoMSstatsFormat: no visible binding for global variable
'missing.col'
SpectronauttoMSstatsFormat: no visible binding for global variable
'fea'
SpectronauttoMSstatsFormat: no visible binding for global variable
'Intensity'
SpectronauttoMSstatsFormat: no visible binding for global variable
'PeptideSequence'
SpectronauttoMSstatsFormat: no visible binding for global variable
'ProteinName'
dataProcess: no visible binding for global variable 'RUN'
dataProcess: no visible binding for global variable 'LABEL'
dataProcessPlots: no visible binding for global variable 'RUN'
dataProcessPlots: no visible binding for global variable 'ABUNDANCE'
dataProcessPlots: no visible binding for global variable 'Name'
dataProcessPlots: no visible binding for global variable 'analysis'
dataProcessPlots: no visible binding for global variable 'Mean'
dataProcessPlots: no visible binding for global variable 'ciw'
groupComparisonPlots: no visible binding for global variable 'Protein'
groupComparisonPlots: no visible binding for global variable 'logFC'
groupComparisonPlots: no visible binding for global variable 'ciw'
linear_quantlim: no visible binding for global variable 'label'
modelBasedQCPlots: no visible binding for global variable 'residual'
nonlinear_quantlim: no visible binding for global variable 'label'
plot_quantlim: no visible binding for global variable 'x'
plot_quantlim: no visible binding for global variable 'y'
plot_quantlim: no visible binding for global variable 'ymin'
plot_quantlim: no visible binding for global variable 'ymax'
plot_quantlim: no visible binding for global variable 'shape'
transformMSnSetToMSstats: no visible global function definition for
'exprs'
transformMSstatsToMSnSet: no visible global function definition for
'sampleNames<-'
transformMSstatsToMSnSet: no visible global function definition for
'featureNames<-'
Undefined global functions or variables:
ABUNDANCE Intensity LABEL Mean Name PeptideSequence Protein
ProteinName RUN Selected_fragments Selected_peptides
aggr_Fragment_Annotation aggr_Peak_Area analysis ciw datafeature
exprs fea featureNames<- grid.layout grid.newpage label logFC
missing.col pushViewport residual sampleNames<- shape weight x y ymax
ymin
* checking Rd files ... OK
* 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
dataProcessPlots 8.62 0.02 15.75
dataProcess 4.74 0.06 24.27
groupComparisonPlots 3.97 0.02 10.50
designSampleSize 2.22 0.00 8.00
modelBasedQCPlots 1.30 0.05 8.06
designSampleSizePlots 1.24 0.01 6.79
quantification 0.81 0.00 6.99
transformMSnSetToMSstats 0.75 0.04 6.78
groupComparison 0.70 0.03 7.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
dataProcessPlots 9.94 0.05 17.03
dataProcess 5.00 0.04 26.28
groupComparisonPlots 4.81 0.00 12.44
designSampleSize 2.64 0.02 9.82
modelBasedQCPlots 1.88 0.02 8.97
designSampleSizePlots 1.06 0.07 8.79
quantification 0.84 0.00 8.31
groupComparison 0.80 0.02 7.39
transformMSnSetToMSstats 0.63 0.06 7.74
* 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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/MSstats.Rcheck/00check.log'
for details.
MSstats.Rcheck/00install.out
install for i386
* installing *source* package 'MSstats' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import 'foreach::accumulate' by 'purrr::accumulate' when loading 'MSstats'
Warning: replacing previous import 'foreach::when' by 'purrr::when' when loading 'MSstats'
** help
*** installing help indices
converting help for package 'MSstats'
finding HTML links ... done
DDARawData html
DDARawData.Skyline html
DIARawData html
DIAUmpiretoMSstatsFormat html
MSstats-package html
MaxQtoMSstatsFormat html
OpenSWATHtoMSstatsFormat html
PDtoMSstatsFormat html
ProgenesistoMSstatsFormat html
SRMRawData html
SkylinetoMSstatsFormat html
SpectronauttoMSstatsFormat html
SpikeInDataLinear html
SpikeInDataNonLinear html
dataProcess html
dataProcessPlots html
designSampleSize html
designSampleSizePlots html
groupComparison html
groupComparisonPlots html
linear_quantlim html
modelBasedQCPlots html
nonlinear_quantlim html
plot_quantlim html
quantification html
transformMSnSetToMSstats html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXA2AK/R.INSTALL35cc1ad33f29/MSstats/man/transformMSnSetToMSstats.Rd:26: missing file link 'MSnSet'
transformMSstatsToMSnSet html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'foreach::accumulate' by 'purrr::accumulate' when loading 'MSstats'
Warning: replacing previous import 'foreach::when' by 'purrr::when' when loading 'MSstats'
In R CMD INSTALL
install for x64
* installing *source* package 'MSstats' ...
** testing if installed package can be loaded
Warning: replacing previous import 'foreach::accumulate' by 'purrr::accumulate' when loading 'MSstats'
Warning: replacing previous import 'foreach::when' by 'purrr::when' when loading 'MSstats'
* MD5 sums
packaged installation of 'MSstats' as MSstats_3.10.6.zip
* DONE (MSstats)
In R CMD INSTALL
In R CMD INSTALL
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MSstats.Rcheck/examples_i386/MSstats-Ex.timings
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MSstats.Rcheck/examples_x64/MSstats-Ex.timings
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