proteoQC 1.10.0
Bo Wen
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/proteoQC | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings proteoQC_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/proteoQC.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proteoQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proteoQC’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘proteoQC’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
extdata 4.0Mb
* 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
* 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 global function definition for ‘par’
addSummaryChart: no visible global function definition for ‘read.delim’
addSummaryChart: no visible global function definition for ‘png’
addSummaryChart: no visible binding for global variable ‘peplength’
addSummaryChart: no visible binding for global variable ‘..count..’
addSummaryChart: no visible global function definition for ‘dev.off’
addSummaryChart: no visible global function definition for ‘quantile’
addSummaryChart: no visible binding for global variable ‘delta’
addSummaryChart: no visible global function definition for ‘hist’
addSummaryChart: no visible global function definition for ‘lines’
addSummaryChart: no visible global function definition for ‘density’
addSummaryChart: no visible global function definition for ‘box’
calcMSQCMetrics: no visible global function definition for ‘read.delim’
calcMSQCMetrics : <anonymous>: no visible global function definition
for ‘write.table’
cntStat: no visible global function definition for ‘read.delim’
combineRun: no visible global function definition for ‘read.table’
getEnzyme: no visible global function definition for ‘read.delim’
getMods: no visible global function definition for ‘read.delim’
ggplot.RT: no visible global function definition for ‘png’
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’
ggplot.RT: no visible global function definition for ‘dev.off’
labelRatio: no visible binding for global variable ‘label’
labelRatio: no visible binding for global variable ‘x’
labelRatio: no visible binding for global variable ‘ratio’
msQC.barplot: no visible global function definition for ‘png’
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’
msQC.barplot: no visible global function definition for ‘dev.off’
msQCpipe: no visible global function definition for ‘read.table’
plotBioRepVenn : <anonymous> : <anonymous>: no visible global function
definition for ‘read.delim’
plotBioRepVenn : <anonymous>: no visible global function definition for
‘png’
plotBioRepVenn : <anonymous>: no visible global function definition for
‘par’
plotBioRepVenn : <anonymous>: no visible global function definition for
‘grid.draw’
plotBioRepVenn : <anonymous>: no visible global function definition for
‘dev.off’
plotFractionAccumulation : <anonymous>: no visible global function
definition for ‘png’
plotFractionAccumulation : <anonymous>: no visible global function
definition for ‘dev.off’
plotFractionIDResult: no visible global function definition for ‘png’
plotFractionIDResult: no visible global function definition for
‘dev.off’
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 global function definition for ‘read.delim’
plotMS1Count: no visible binding for global variable ‘MS1QC’
plotMS1Count: no visible global function definition for ‘png’
plotMS1Count: no visible global function definition for ‘dev.off’
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 global function definition for
‘read.delim’
plotMS1CountErrorBar: no visible binding for global variable ‘MS1QC’
plotMS1CountErrorBar : <anonymous>: no visible global function
definition for ‘sd’
plotMS1CountErrorBar: no visible global function definition for ‘png’
plotMS1CountErrorBar: no visible binding for global variable ‘val’
plotMS1CountErrorBar: no visible binding for global variable ‘se’
plotMS1CountErrorBar: no visible global function definition for
‘dev.off’
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 global function definition for ‘read.delim’
plotMS1Error: no visible binding for global variable ‘peptide_summary’
plotMS1Error: no visible binding for global variable ‘curenv’
plotMS1Error : <anonymous>: no visible global function definition for
‘read.delim’
plotMS1Error : <anonymous>: no visible binding for global variable
‘curenv’
plotMS1Error : <anonymous>: no visible global function definition for
‘quantile’
plotMS1Error: no visible global function definition for ‘png’
plotMS1Error: no visible global function definition for ‘dev.off’
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 global function definition for ‘read.delim’
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 global function definition for
‘read.delim’
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 global function definition for ‘read.delim’
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 global function definition for ‘read.delim’
plotMS1boxplot: no visible binding for global variable ‘MS1QC’
plotMS1boxplot: no visible global function definition for ‘png’
plotMS1boxplot: no visible global function definition for ‘dev.off’
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 : <anonymous>: no visible global function definition for
‘read.delim’
plotMS2Error: no visible global function definition for ‘png’
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: no visible global function definition for ‘dev.off’
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 global function definition for
‘read.delim’
plotMS2Error_obsolete: no visible binding for global variable
‘peptide_summary’
plotMS2Error_obsolete : <anonymous>: no visible global function
definition for ‘quantile’
plotMS2Error_obsolete : <anonymous>: no visible global function
definition for ‘read.delim’
plotMS2Error_obsolete: no visible global function definition for ‘png’
plotMS2Error_obsolete: no visible global function definition for
‘dev.off’
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 global function definition for ‘read.delim’
plotMS2PeakFreq: no visible binding for global variable ‘MS2QC’
plotMS2PeakFreq: no visible global function definition for ‘png’
plotMS2PeakFreq: no visible global function definition for ‘dev.off’
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 global function definition for ‘read.delim’
plotMS2boxplot: no visible binding for global variable ‘MS2QC’
plotMS2boxplot: no visible global function definition for ‘png’
plotMS2boxplot: no visible global function definition for ‘dev.off’
plotSampleIDResultErrorBar: no visible binding for global variable
‘fraction’
plotSampleIDResultErrorBar : <anonymous>: no visible global function
definition for ‘sd’
plotSampleIDResultErrorBar: no visible global function definition for
‘png’
plotSampleIDResultErrorBar: no visible binding for global variable
‘val’
plotSampleIDResultErrorBar: no visible binding for global variable ‘se’
plotSampleIDResultErrorBar: no visible global function definition for
‘dev.off’
plotSampleVenn : <anonymous>: no visible global function definition for
‘read.delim’
plotSampleVenn: no visible global function definition for ‘png’
plotSampleVenn: no visible global function definition for ‘par’
plotSampleVenn: no visible global function definition for ‘grid.draw’
plotSampleVenn: no visible global function definition for ‘dev.off’
plotTechRepVenn : <anonymous> : <anonymous>: no visible global function
definition for ‘read.delim’
plotTechRepVenn : <anonymous>: no visible global function definition
for ‘png’
plotTechRepVenn : <anonymous>: no visible global function definition
for ‘par’
plotTechRepVenn : <anonymous>: no visible global function definition
for ‘grid.draw’
plotTechRepVenn : <anonymous>: no visible global function definition
for ‘dev.off’
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’
runTandem: no visible global function definition for ‘read.table’
showEnzyme: no visible global function definition for ‘read.delim’
showMods: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
..count.. MS1QC MS2QC V1 V2 V3 V4 V5 bioRep box curenv delta density
dev.off error fractile fraction grid.draw hist label lines par
peplength peptide_summary png quantile ratio read.delim read.table sd
se techRep val write.table x y
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "box", "hist", "lines", "par")
importFrom("stats", "density", "quantile", "sd")
importFrom("utils", "read.delim", "read.table", "write.table")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘proteoQC/libs/proteoQC.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Object: ‘utilities.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/proteoQC.Rcheck/00check.log’
for details.
* installing *source* package ‘proteoQC’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c utilities.cpp -o utilities.o
utilities.cpp: In function ‘SEXPREC* LableRatio_Cpp(SEXP, SEXP, SEXP)’:
utilities.cpp:137:6: warning: variable ‘ms2flag’ set but not used [-Wunused-but-set-variable]
int ms2flag=0;
^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o proteoQC.so utilities.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/proteoQC.Rcheck/proteoQC/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (proteoQC)