Bo Wen
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/proteoQC |
| Branch: RELEASE_3_6 |
| Last Commit: 51713ac |
| Last Changed Date: 2017-10-30 12:40:15 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:24:21 -0400 (Thu, 12 Apr 2018).
| Package 1081/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proteoQC 1.14.0 Bo Wen
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: proteoQC |
| Version: 1.14.0 |
| Command: rm -rf proteoQC.buildbin-libdir proteoQC.Rcheck && mkdir proteoQC.buildbin-libdir proteoQC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=proteoQC.buildbin-libdir proteoQC_1.14.0.tar.gz >proteoQC.Rcheck\00install.out 2>&1 && cp proteoQC.Rcheck\00install.out proteoQC-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=proteoQC.buildbin-libdir --install="check:proteoQC-install.out" --force-multiarch --no-vignettes --timings proteoQC_1.14.0.tar.gz |
| StartedAt: 2018-04-12 02:18:13 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:23:21 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 308.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proteoQC.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### rm -rf proteoQC.buildbin-libdir proteoQC.Rcheck && mkdir proteoQC.buildbin-libdir proteoQC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=proteoQC.buildbin-libdir proteoQC_1.14.0.tar.gz >proteoQC.Rcheck\00install.out 2>&1 && cp proteoQC.Rcheck\00install.out proteoQC-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=proteoQC.buildbin-libdir --install="check:proteoQC-install.out" --force-multiarch --no-vignettes --timings proteoQC_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/proteoQC.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 'proteoQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'proteoQC' version '1.14.0'
* 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 'proteoQC' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.3Mb
sub-directories of 1Mb or more:
doc 2.5Mb
extdata 3.9Mb
* 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
calcMSQCMetrics : <anonymous>: warning in readMSData(x, msLevel = 1):
partial argument match of 'msLevel' to 'msLevel.'
calcMSQCMetrics : <anonymous>: warning in readMSData(x, msLevel = 2):
partial argument match of 'msLevel' to 'msLevel.'
addSummaryChart: no visible binding for global variable 'peplength'
addSummaryChart: no visible binding for global variable '..count..'
addSummaryChart: no visible binding for global variable 'delta'
chargeStat: no visible global function definition for 'readMgfData'
chargeStat: no visible global function definition for 'precursorCharge'
ggplot.RT: no visible binding for global variable 'x'
ggplot.RT: no visible binding for global variable 'y'
ggplot.RT: no visible binding for global variable 'techRep'
ggplot.RT: no visible binding for global variable 'bioRep'
labelRatio: no visible global function definition for 'readMgfData'
labelRatio: no visible binding for global variable 'iTRAQ4'
labelRatio: no visible binding for global variable 'iTRAQ8'
labelRatio: no visible binding for global variable 'TMT6'
labelRatio: no visible binding for global variable 'TMT10'
labelRatio: no visible global function definition for 'exprs'
labelRatio: no visible global function definition for 'quantify'
labelRatio: no visible binding for global variable 'Tag'
labelRatio: no visible binding for global variable 'Intensity'
labelRatio: no visible binding for global variable 'ratio'
labelRatio: no visible binding for global variable 'label'
msQC.barplot: no visible binding for global variable 'x'
msQC.barplot: no visible binding for global variable 'y'
msQC.barplot: no visible binding for global variable 'label'
plotBioRepVenn : <anonymous>: no visible global function definition for
'grid.draw'
plotMS1Count: no visible binding for global variable 'bioRep'
plotMS1Count: no visible binding for global variable 'techRep'
plotMS1Count: no visible binding for global variable 'fraction'
plotMS1Count: no visible binding for global variable 'MS1QC'
plotMS1CountErrorBar: no visible binding for global variable 'bioRep'
plotMS1CountErrorBar: no visible binding for global variable 'techRep'
plotMS1CountErrorBar: no visible binding for global variable 'fraction'
plotMS1CountErrorBar: no visible binding for global variable 'MS1QC'
plotMS1CountErrorBar: no visible binding for global variable 'val'
plotMS1CountErrorBar: no visible binding for global variable 'se'
plotMS1Error: no visible binding for '<<-' assignment to 'curenv'
plotMS1Error: no visible binding for global variable 'bioRep'
plotMS1Error: no visible binding for global variable 'techRep'
plotMS1Error: no visible binding for global variable 'fraction'
plotMS1Error: no visible binding for global variable 'peptide_summary'
plotMS1Error: no visible binding for global variable 'curenv'
plotMS1Error : <anonymous>: no visible binding for global variable
'curenv'
plotMS1IonCount: no visible binding for global variable 'bioRep'
plotMS1IonCount: no visible binding for global variable 'techRep'
plotMS1IonCount: no visible binding for global variable 'fraction'
plotMS1IonCount: no visible binding for global variable 'MS1QC'
plotMS1PeaksCount: no visible binding for global variable 'bioRep'
plotMS1PeaksCount: no visible binding for global variable 'techRep'
plotMS1PeaksCount: no visible binding for global variable 'fraction'
plotMS1PeaksCount: no visible binding for global variable 'MS1QC'
plotMS1TIC: no visible binding for global variable 'bioRep'
plotMS1TIC: no visible binding for global variable 'techRep'
plotMS1TIC: no visible binding for global variable 'fraction'
plotMS1TIC: no visible binding for global variable 'MS1QC'
plotMS1boxplot: no visible binding for global variable 'bioRep'
plotMS1boxplot: no visible binding for global variable 'techRep'
plotMS1boxplot: no visible binding for global variable 'fraction'
plotMS1boxplot: no visible binding for global variable 'MS1QC'
plotMS2Error: no visible binding for global variable 'bioRep'
plotMS2Error: no visible binding for global variable 'techRep'
plotMS2Error: no visible binding for global variable 'fraction'
plotMS2Error: no visible binding for global variable 'V1'
plotMS2Error: no visible binding for global variable 'V2'
plotMS2Error: no visible binding for global variable 'V3'
plotMS2Error: no visible binding for global variable 'V4'
plotMS2Error: no visible binding for global variable 'V5'
plotMS2Error_obsolete: no visible binding for global variable 'bioRep'
plotMS2Error_obsolete: no visible binding for global variable 'techRep'
plotMS2Error_obsolete: no visible binding for global variable
'fraction'
plotMS2Error_obsolete: no visible binding for global variable
'peptide_summary'
plotMS2PeakFreq: no visible binding for global variable 'bioRep'
plotMS2PeakFreq: no visible binding for global variable 'techRep'
plotMS2PeakFreq: no visible binding for global variable 'fraction'
plotMS2PeakFreq: no visible binding for global variable 'MS2QC'
plotMS2boxplot: no visible binding for global variable 'bioRep'
plotMS2boxplot: no visible binding for global variable 'techRep'
plotMS2boxplot: no visible binding for global variable 'fraction'
plotMS2boxplot: no visible binding for global variable 'MS2QC'
plotSampleIDResultErrorBar: no visible binding for global variable
'fraction'
plotSampleIDResultErrorBar: no visible binding for global variable
'val'
plotSampleIDResultErrorBar: no visible binding for global variable 'se'
plotSampleVenn: no visible global function definition for 'grid.draw'
plotTechRepVenn : <anonymous>: no visible global function definition
for 'grid.draw'
qcHist: no visible binding for global variable 'error'
qcHist: no visible binding for global variable 'techRep'
qcHist: no visible binding for global variable 'bioRep'
qcHist2: no visible binding for global variable 'error'
qcHist2: no visible binding for global variable 'fractile'
Undefined global functions or variables:
..count.. Intensity MS1QC MS2QC TMT10 TMT6 Tag V1 V2 V3 V4 V5 bioRep
curenv delta error exprs fractile fraction grid.draw iTRAQ4 iTRAQ8
label peplength peptide_summary precursorCharge quantify ratio
readMgfData se techRep val x y
* 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 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
labelRatio 15.56 0.08 37.01
chargeStat 13.24 0.05 13.30
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
labelRatio 17.21 0.05 43.51
chargeStat 14.58 0.05 14.62
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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 ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/proteoQC.Rcheck/00check.log'
for details.
proteoQC.Rcheck/00install.out
install for i386
* installing *source* package 'proteoQC' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'proteoQC'
finding HTML links ... done
addSummaryChart html
calcMSQCMetrics html
chargeStat html
cntStat html
combineRun html
createTargetDecoyDB html
getEnzyme html
getMods html
labelRatio html
loadmsQCres html
msQCpipe html
plotBioRepVenn html
plotFractionIDResult html
plotMS1Error html
plotMS2Error html
plotMS2Error_obsolete html
plotSampleIDResultErrorBar html
plotSampleVenn html
plotTechRepVenn html
print.msQCres html
proteinGroup html
reportHTML html
runTandem html
showEnzyme html
showMods html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'proteoQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proteoQC' as proteoQC_1.14.0.zip
* DONE (proteoQC)
In R CMD INSTALL
In R CMD INSTALL
|
proteoQC.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("proteoQC")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
This is MSnbase version 2.4.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
RUNIT TEST PROTOCOL -- Thu Apr 12 02:23:11 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
proteoQC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.39 0.32 6.51
|
proteoQC.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("proteoQC")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
This is MSnbase version 2.4.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
RUNIT TEST PROTOCOL -- Thu Apr 12 02:23:17 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
proteoQC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
5.26 0.26 5.68
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proteoQC.Rcheck/examples_i386/proteoQC-Ex.timings
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proteoQC.Rcheck/examples_x64/proteoQC-Ex.timings
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