Package: ProteoMM

Version: 1.1.1

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_1.1.1.tar.gz

StartedAt: 2019-04-09 03:02:26 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:04:54 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 148.3 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_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ProteoMM.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.1.1’
* 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       33.189  0.232  33.524
subset_proteins             10.654  0.118  10.821
prot_level_multiMat_PresAbs 10.436  0.110  10.598
get_presAbs_prots            6.799  0.129   6.945
plot_volcano_wLab            6.764  0.081   6.873
peptideLevel_PresAbsDE       6.352  0.167   6.529
MBimpute                     6.007  0.208   6.234
plot_volcano                 6.062  0.081   6.165
peptideLevel_DE              5.519  0.082   5.614
* 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’ ...
** 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	6.007	0.208	6.234
convert_log2	0.008	0.001	0.010
eig_norm1	4.366	0.083	4.461
eig_norm2	4.538	0.080	4.632
eigen_pi	0.012	0.002	0.015
g.test	0.003	0.000	0.003
get_presAbs_prots	6.799	0.129	6.945
makeLMFormula	0.001	0.000	0.001
make_intencities	0.006	0.001	0.006
make_meta	0.006	0.001	0.008
peptideLevel_DE	5.519	0.082	5.614
peptideLevel_PresAbsDE	6.352	0.167	6.529
plot_3_pep_trends_NOfile	4.007	0.075	4.097
plot_volcano	6.062	0.081	6.165
plot_volcano_wLab	6.764	0.081	6.873
prot_level_multiMat_PresAbs	10.436	0.110	10.598
prot_level_multi_part	33.189	0.232	33.524
subset_proteins	10.654	0.118	10.821