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CHECK report for ProteoMM on celaya2

This page was generated on 2019-10-16 13:03:37 -0400 (Wed, 16 Oct 2019).

Package 1268/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProteoMM 1.2.0
Yuliya V Karpievitch
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ProteoMM
Branch: RELEASE_3_9
Last Commit: be669a5
Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ProteoMM
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ProteoMM_1.2.0.tar.gz
StartedAt: 2019-10-16 05:48:00 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:51:20 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 200.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ProteoMM.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ProteoMM_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ProteoMM.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProteoMM/DESCRIPTION’ ... OK
* this is package ‘ProteoMM’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ProteoMM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
prot_level_multi_part       43.130  0.359  43.504
prot_level_multiMat_PresAbs 13.647  0.261  13.913
subset_proteins             12.780  0.261  13.046
peptideLevel_PresAbsDE       9.992  0.236  10.232
get_presAbs_prots            9.710  0.269   9.983
plot_volcano_wLab            8.666  0.183   8.853
peptideLevel_DE              8.077  0.138   8.218
MBimpute                     7.478  0.465   7.944
plot_volcano                 7.680  0.186   7.870
eig_norm2                    6.055  0.169   6.226
eig_norm1                    5.762  0.178   5.941
plot_3_pep_trends_NOfile     5.381  0.106   5.491
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ProteoMM.Rcheck/00check.log’
for details.



Installation output

ProteoMM.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ProteoMM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ProteoMM’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (ProteoMM)

Tests output


Example timings

ProteoMM.Rcheck/ProteoMM-Ex.timings

nameusersystemelapsed
MBimpute7.4780.4657.944
convert_log20.0120.0040.015
eig_norm15.7620.1785.941
eig_norm26.0550.1696.226
eigen_pi0.0160.0030.020
g.test0.0050.0010.005
get_presAbs_prots9.7100.2699.983
makeLMFormula0.0010.0000.002
make_intencities0.0120.0030.014
make_meta0.0110.0030.014
peptideLevel_DE8.0770.1388.218
peptideLevel_PresAbsDE 9.992 0.23610.232
plot_3_pep_trends_NOfile5.3810.1065.491
plot_volcano7.6800.1867.870
plot_volcano_wLab8.6660.1838.853
prot_level_multiMat_PresAbs13.647 0.26113.913
prot_level_multi_part43.130 0.35943.504
subset_proteins12.780 0.26113.046