Package: ProteoMM

Version: 1.0.1

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_1.0.1.tar.gz

StartedAt: 2019-04-16 02:03:26 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:05:50 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 144.0 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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ProteoMM.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.1’
* 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       30.899  0.180  31.170
prot_level_multiMat_PresAbs 10.256  0.127  10.436
subset_proteins              9.689  0.160   9.876
get_presAbs_prots            7.825  0.166   8.026
peptideLevel_PresAbsDE       7.003  0.134   7.166
plot_volcano_wLab            6.909  0.092   7.027
plot_volcano                 6.287  0.097   6.414
MBimpute                     5.936  0.160   6.138
peptideLevel_DE              5.986  0.093   6.095
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘ProteoMM’ ...
** 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
* DONE (ProteoMM)

name	user	system	elapsed
MBimpute	5.936	0.160	6.138
convert_log2	0.007	0.001	0.007
eig_norm1	4.541	0.084	4.649
eig_norm2	4.333	0.079	4.432
eigen_pi	0.011	0.002	0.012
g.test	0.005	0.000	0.006
get_presAbs_prots	7.825	0.166	8.026
makeLMFormula	0	0	0
make_intencities	0.006	0.001	0.007
make_meta	0.006	0.001	0.007
peptideLevel_DE	5.986	0.093	6.095
peptideLevel_PresAbsDE	7.003	0.134	7.166
plot_3_pep_trends_NOfile	4.096	0.053	4.163
plot_volcano	6.287	0.097	6.414
plot_volcano_wLab	6.909	0.092	7.027
prot_level_multiMat_PresAbs	10.256	0.127	10.436
prot_level_multi_part	30.899	0.180	31.170
subset_proteins	9.689	0.160	9.876