Bo Wen
| Snapshot Date: 2019-10-01 17:01:25 -0400 (Tue, 01 Oct 2019) |
| URL: https://git.bioconductor.org/packages/proteoQC |
| Branch: RELEASE_3_9 |
| Last Commit: 20a400d |
| Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-02 12:30:46 -0400 (Wed, 02 Oct 2019).
| Package 1269/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proteoQC 1.20.0 Bo Wen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: proteoQC |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proteoQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings proteoQC_1.20.0.tar.gz |
| StartedAt: 2019-10-02 06:01:25 -0400 (Wed, 02 Oct 2019) |
| EndedAt: 2019-10-02 06:06:20 -0400 (Wed, 02 Oct 2019) |
| EllapsedTime: 295.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proteoQC.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proteoQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings proteoQC_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/proteoQC.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '1.20.0' * 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 ... 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 ... NOTE Found the following apparent S3 methods exported but not registered: print.msQCres See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE calcMSQCMetrics :: warning in readMSData(x, msLevel = 1): partial argument match of 'msLevel' to 'msLevel.' calcMSQCMetrics : : 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 : : 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 : : 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 : : 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed labelRatio 6.18 0.03 30.61 chargeStat 5.16 0.23 5.79 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed labelRatio 7.00 0.11 38.20 chargeStat 6.54 0.04 6.59 * 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-3.9-bioc/meat/proteoQC.Rcheck/00check.log' for details.
proteoQC.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/proteoQC_1.20.0.tar.gz && rm -rf proteoQC.buildbin-libdir && mkdir proteoQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proteoQC.buildbin-libdir proteoQC_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL proteoQC_1.20.0.zip && rm proteoQC_1.20.0.tar.gz proteoQC_1.20.0.zip
###
##############################################################################
##############################################################################
% 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 4556k 100 4556k 0 0 27.3M 0 --:--:-- --:--:-- --:--:-- 28.5M
install for i386
* installing *source* package 'proteoQC' ...
** using staged installation
** R
** inst
** byte-compile and prepare 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 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 'proteoQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proteoQC' as proteoQC_1.20.0.zip
* DONE (proteoQC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'proteoQC' successfully unpacked and MD5 sums checked
|
proteoQC.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
This is MSnbase version 2.10.1
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 -- Wed Oct 02 06:06:02 2019
***********************************************
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 0.35 5.61
|
proteoQC.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
This is MSnbase version 2.10.1
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 -- Wed Oct 02 06:06:09 2019
***********************************************
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
4.92 0.48 5.59
|
|
proteoQC.Rcheck/examples_i386/proteoQC-Ex.timings
|
proteoQC.Rcheck/examples_x64/proteoQC-Ex.timings
|