Meena Choi
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MSstats |
| Branch: RELEASE_3_9 |
| Last Commit: fc3245c |
| Last Changed Date: 2019-08-15 20:22:14 -0400 (Thu, 15 Aug 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:28:44 -0400 (Wed, 16 Oct 2019).
| Package 1058/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSstats 3.16.2 Meena Choi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: MSstats |
| Version: 3.16.2 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSstats_3.16.2.tar.gz |
| StartedAt: 2019-10-16 05:26:41 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:45:37 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1135.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSstats.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSstats_3.16.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MSstats.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 'MSstats/DESCRIPTION' ... OK
* this is package 'MSstats' version '3.16.2'
* package encoding: UTF-8
* 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:
Warning: replacing previous import 'MASS::select' by 'dplyr::select' when loading 'MSstats'
See 'C:/Users/biocbuild/bbs-3.9-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
* 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 ... 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'
.runQuantification: no visible binding for global variable
'datafeature'
.runQuantification: no visible binding for global variable 'ount'
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'
OpenMStoMSstatsFormat: no visible binding for global variable
'missing.col'
OpenMStoMSstatsFormat: no visible binding for global variable 'fea'
OpenMStoMSstatsFormat: no visible binding for global variable
'Intensity'
OpenMStoMSstatsFormat: no visible binding for global variable
'PeptideSequence'
OpenMStoMSstatsFormat: no visible binding for global variable
'ProteinName'
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'
PDtoMSstatsFormat: no visible binding for global variable 'fea'
PDtoMSstatsFormat: no visible binding for global variable 'Intensity'
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'
calc_fvar: no visible binding for global variable '.resid'
calc_fvar: no visible binding for global variable 'is_olr'
calc_fvar: no visible binding for global variable 'log2inty'
calc_fvar: no visible binding for global variable 'feature'
calc_fvar: no visible binding for global variable 'nb_run'
calc_fvar: no visible binding for global variable 'resid_null'
calc_fvar: no visible binding for global variable 'svar_feature'
calc_fvar: no visible binding for global variable 'svar_ref'
dataProcess: no visible binding for global variable 'FEATURE'
dataProcess: no visible binding for global variable 'ncount'
dataProcess: no visible binding for global variable 'ABUNDANCE'
dataProcess: no visible binding for global variable 'RUN'
dataProcess: no visible binding for global variable 'FRACTION'
dataProcess: no visible binding for global variable 'PROTEIN'
dataProcess: no visible binding for global variable 'INTENSITY'
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'
designSampleSizeClassificationPlots: no visible binding for global
variable 'Train_size'
designSampleSizeClassificationPlots: no visible binding for global
variable 'Protein_number'
flag_noninf_data: no visible binding for global variable 'PROTEIN'
flag_noninf_data: no visible binding for global variable 'PEPTIDE'
flag_noninf_data: no visible binding for global variable 'FEATURE'
flag_noninf_data: no visible binding for global variable 'originalRUN'
flag_noninf_data: no visible binding for global variable 'LABEL'
flag_noninf_data: no visible binding for global variable 'ABUNDANCE'
flag_noninf_data: no visible binding for global variable 'censored'
flag_noninf_data: no visible binding for global variable 'log2inty'
flag_noninf_data: no visible binding for global variable 'is_censored'
flag_noninf_data: no visible binding for global variable 'is_obs'
flag_noninf_data: no visible binding for global variable 'protein'
flag_noninf_data: no visible binding for global variable 'peptide'
flag_noninf_data: no visible binding for global variable 'feature'
flag_noninf_data: no visible binding for global variable 'run'
flag_noninf_data: no visible binding for global variable 'label'
flag_noninf_data: no visible binding for global variable 'nb_run'
flag_noninf_data: no visible binding for global variable 'nb_feature'
flag_noninf_data: no visible binding for global variable 'nb_obs'
flag_noninf_data: no visible binding for global variable 'nb_full'
flag_noninf_data: no visible binding for global variable 'pi_obs'
flag_noninf_data: no visible binding for global variable 'min_obs'
flag_noninf_data: no visible binding for global variable 'is_lowcvr'
flag_noninf_data: no visible binding for global variable
'cover_feature'
flag_noninf_data: no visible binding for global variable 'rlm_fit'
flag_noninf_data: no visible binding for global variable 's_resid'
flag_noninf_data: no visible binding for global variable 'df_resid'
flag_noninf_data: no visible binding for global variable 'var_resid_eb'
flag_noninf_data: no visible binding for global variable 's_resid_eb'
flag_noninf_data: no visible binding for global variable 'is_olr'
flag_noninf_data: no visible binding for global variable 'var_feature'
flag_noninf_data: no visible binding for global variable 'svar_feature'
flag_noninf_data_nbftr: no visible binding for global variable
'PROTEIN'
flag_noninf_data_nbftr: no visible binding for global variable
'PEPTIDE'
flag_noninf_data_nbftr: no visible binding for global variable
'FEATURE'
flag_noninf_data_nbftr: no visible binding for global variable
'originalRUN'
flag_noninf_data_nbftr: no visible binding for global variable 'LABEL'
flag_noninf_data_nbftr: no visible binding for global variable
'ABUNDANCE'
flag_noninf_data_nbftr: no visible binding for global variable
'censored'
flag_noninf_data_nbftr: no visible binding for global variable
'log2inty'
flag_noninf_data_nbftr: no visible binding for global variable
'is_censored'
flag_noninf_data_nbftr: no visible binding for global variable 'is_obs'
flag_noninf_data_nbftr: no visible binding for global variable
'protein'
flag_noninf_data_nbftr: no visible binding for global variable
'peptide'
flag_noninf_data_nbftr: no visible binding for global variable
'feature'
flag_noninf_data_nbftr: no visible binding for global variable 'run'
flag_noninf_data_nbftr: no visible binding for global variable 'label'
flag_noninf_data_nbftr: no visible binding for global variable
'nb_feature'
flag_noninf_data_nbftr: no visible binding for global variable 'nb_run'
flag_noninf_data_nbftr: no visible binding for global variable 'nb_obs'
flag_noninf_data_nbftr: no visible binding for global variable
'nb_full'
flag_noninf_data_nbftr: no visible binding for global variable 'pi_obs'
flag_noninf_data_nbftr: no visible binding for global variable
'min_obs'
flag_noninf_data_nbftr: no visible binding for global variable
'is_lowcvr'
flag_noninf_data_nbftr: no visible binding for global variable
'cover_feature'
flag_noninf_data_nbftr: no visible binding for global variable
'rlm_fit'
flag_noninf_data_nbftr: no visible binding for global variable
's_resid'
flag_noninf_data_nbftr: no visible binding for global variable
'df_resid'
flag_noninf_data_nbftr: no visible binding for global variable
'var_resid_eb'
flag_noninf_data_nbftr: no visible binding for global variable
's_resid_eb'
flag_noninf_data_nbftr: no visible binding for global variable 'is_olr'
flag_noninf_data_nbftr: no visible binding for global variable
'var_feature'
flag_noninf_data_nbftr: no visible binding for global variable
'svar_feature'
flag_outlier: no visible binding for global variable '.resid'
flag_outlier: no visible binding for global variable 'run'
flag_outlier: no visible binding for global variable 'feature'
flag_outlier: no visible binding for global variable 'is_olr'
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'
Undefined global functions or variables:
.resid ABUNDANCE FEATURE FRACTION INTENSITY Intensity LABEL Mean Name
PEPTIDE PROTEIN PeptideSequence Protein ProteinName Protein_number
RUN Selected_fragments Selected_peptides Train_size
aggr_Fragment_Annotation aggr_Peak_Area analysis censored ciw
cover_feature datafeature df_resid fea feature is_censored is_lowcvr
is_obs is_olr label log2inty logFC min_obs missing.col nb_feature
nb_full nb_obs nb_run ncount originalRUN ount peptide pi_obs protein
resid_null residual rlm_fit run s_resid s_resid_eb shape svar_feature
svar_ref var_feature var_resid_eb 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
designSampleSizeClassificationPlots 268.85 0.20 269.05
designSampleSizeClassification 262.87 0.69 264.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
designSampleSizeClassificationPlots 229.03 0.20 231.36
designSampleSizeClassification 225.41 0.46 225.89
dataProcessPlots 5.33 0.01 5.34
* 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-3.9-bioc/meat/MSstats.Rcheck/00check.log'
for details.
MSstats.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MSstats_3.16.2.tar.gz && rm -rf MSstats.buildbin-libdir && mkdir MSstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstats.buildbin-libdir MSstats_3.16.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MSstats_3.16.2.zip && rm MSstats_3.16.2.tar.gz MSstats_3.16.2.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 205k 100 205k 0 0 3551k 0 --:--:-- --:--:-- --:--:-- 4023k
install for i386
* installing *source* package 'MSstats' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'MASS::select' by 'dplyr::select' 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
OpenMStoMSstatsFormat html
OpenSWATHtoMSstatsFormat html
PDtoMSstatsFormat html
ProgenesistoMSstatsFormat html
SRMRawData html
SkylinetoMSstatsFormat html
SpectronauttoMSstatsFormat html
SpikeInDataLinear html
SpikeInDataNonLinear html
dataProcess html
dataProcessPlots html
designSampleSize html
designSampleSizeClassification html
designSampleSizeClassificationPlots html
designSampleSizePlots html
groupComparison html
groupComparisonPlots html
linear_quantlim html
modelBasedQCPlots html
nonlinear_quantlim html
plot_quantlim html
quantification html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'MASS::select' by 'dplyr::select' when loading 'MSstats'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'MASS::select' by 'dplyr::select' when loading 'MSstats'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'MSstats' ...
** testing if installed package can be loaded
Warning: replacing previous import 'MASS::select' by 'dplyr::select' when loading 'MSstats'
* MD5 sums
packaged installation of 'MSstats' as MSstats_3.16.2.zip
* DONE (MSstats)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MSstats' successfully unpacked and MD5 sums checked
|
MSstats.Rcheck/examples_i386/MSstats-Ex.timings
|
MSstats.Rcheck/examples_x64/MSstats-Ex.timings
|