MSstats 3.2.1
Meena Choi
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MSstats | | Last Changed Rev: 114241 / Revision: 116712 | | Last Changed Date: 2016-03-03 20:20:26 -0800 (Thu, 03 Mar 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSstats_3.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MSstats.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘3.2.1’
* 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 ‘MSstats’ can be installed ... [13s/13s] WARNING
Found the following significant warnings:
Warning: replacing previous import ‘reshape::melt’ by ‘data.table::melt’ when loading ‘MSstats’
See ‘/home/biocbuild/bbs-3.2-bioc/meat/MSstats.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘grid’ which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
‘Rcpp’ ‘grid’ ‘reshape2’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dataProcessPlots: warning in scale_y_continuous("Log2-intensities",
limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
'limits'
dataProcessPlots: warning in scale_y_continuous("Log10-intensities",
limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
'limits'
dataProcessPlots: warning in scale_y_continuous("Log2-Ratio(L/H)",
limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
'limits'
dataProcessPlots: warning in scale_y_continuous("Log10-Ratio(L/H)",
limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
'limits'
groupComparisonPlots: warning in scale_y_continuous("-Log2 (adjusted
p-value)", limit = c(y.limdown, y.limup)): partial argument match of
'limit' to 'limits'
groupComparisonPlots: warning in scale_y_continuous("-Log10 (adjusted
p-value)", limit = c(y.limdown, y.limup)): partial argument match of
'limit' to 'limits'
groupComparisonPlots: warning in scale_x_continuous("Log2 fold change",
limit = c(-x.lim, x.lim)): partial argument match of 'limit' to
'limits'
groupComparisonPlots: warning in scale_x_continuous("Log10 fold
change", limit = c(-x.lim, x.lim)): partial argument match of 'limit'
to 'limits'
groupComparisonPlots: warning in scale_y_continuous("Log2-Fold Change",
limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
'limits'
groupComparisonPlots: warning in scale_y_continuous("Log10-Fold
Change", limit = c(y.limdown, y.limup)): partial argument match of
'limit' to 'limits'
modelBasedQCPlots: warning in scale_y_continuous("Residuals", limit =
c(y.limdown, y.limup)): partial argument match of 'limit' to 'limits'
modelBasedQCPlots: warning in scale_x_continuous("Predicted Abundance",
limit = c(x.limdown, x.limup)): partial argument match of 'limit' to
'limits'
.feature_selection: no visible binding for global variable ‘PROTEIN’
.feature_selection: no visible binding for global variable ‘PEPTIDE’
.feature_selection: no visible binding for global variable ‘FEATURE’
.feature_selection: no visible binding for global variable
‘Protein_Peptide’
.feature_selection: no visible binding for global variable
‘Protein_Feature’
.feature_selection: no visible binding for global variable ‘LABEL’
.feature_selection: no visible binding for global variable ‘GROUP’
.feature_selection: no visible binding for global variable ‘Label’
.feature_selection: no visible binding for global variable
‘Protein.Peptide’
.feature_selection: no visible binding for global variable ‘Protein’
.feature_selection: no visible binding for global variable ‘Peptide’
.feature_selection: no visible binding for global variable
‘Protein.Feature’
.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 ‘viewport’
.multiplot: no visible global function definition for ‘grid.layout’
.runQuantification: no visible binding for global variable
‘datafeature’
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 ‘imputed’
dataProcessPlots: no visible binding for global variable ‘analysis’
dataProcessPlots: no visible binding for global variable ‘LABEL’
dataProcessPlots: no visible binding for global variable ‘dot.size’
groupComparisonPlots: no visible binding for global variable ‘Protein’
groupComparisonPlots: no visible binding for global variable ‘logFC’
groupComparisonPlots: no visible binding for global variable ‘ciw’
transformMSnSetToMSstats: no visible global function definition for
‘pData’
transformMSnSetToMSstats: no visible global function definition for
‘exprs’
transformMSstatsToMSnSet: no visible global function definition for
‘sampleNames<-’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/22s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
dataProcessPlots 6.213 0.061 6.313
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/MSstats.Rcheck/00check.log’
for details.
* installing *source* package ‘MSstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘reshape::melt’ by ‘data.table::melt’ when loading ‘MSstats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘reshape::melt’ by ‘data.table::melt’ when loading ‘MSstats’
* DONE (MSstats)