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

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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.

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### Running command:
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###   /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)

name	user	system	elapsed
MBimpute	7.478	0.465	7.944
convert_log2	0.012	0.004	0.015
eig_norm1	5.762	0.178	5.941
eig_norm2	6.055	0.169	6.226
eigen_pi	0.016	0.003	0.020
g.test	0.005	0.001	0.005
get_presAbs_prots	9.710	0.269	9.983
makeLMFormula	0.001	0.000	0.002
make_intencities	0.012	0.003	0.014
make_meta	0.011	0.003	0.014
peptideLevel_DE	8.077	0.138	8.218
peptideLevel_PresAbsDE	9.992	0.236	10.232
plot_3_pep_trends_NOfile	5.381	0.106	5.491
plot_volcano	7.680	0.186	7.870
plot_volcano_wLab	8.666	0.183	8.853
prot_level_multiMat_PresAbs	13.647	0.261	13.913
prot_level_multi_part	43.130	0.359	43.504
subset_proteins	12.780	0.261	13.046