Package: ProteoMM

Version: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2020-01-16 07:43:58 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:47:31 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 213.0 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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ProteoMM.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.0’
* 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 (user + system) or elapsed time > 5s
                              user system elapsed
prot_level_multi_part       43.817  0.376  44.209
prot_level_multiMat_PresAbs 14.618  0.238  14.866
subset_proteins             14.087  0.283  14.376
get_presAbs_prots           10.489  0.259  10.754
peptideLevel_PresAbsDE      10.395  0.216  10.618
plot_volcano_wLab            9.276  0.146   9.427
MBimpute                     8.709  0.429   9.142
peptideLevel_DE              8.514  0.159   8.678
plot_volcano                 8.349  0.173   8.527
eig_norm1                    6.512  0.190   6.706
eig_norm2                    6.115  0.124   6.244
plot_3_pep_trends_NOfile     5.685  0.102   5.791
* 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-3.11-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/4.0/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	8.709	0.429	9.142
convert_log2	0.015	0.002	0.017
eig_norm1	6.512	0.190	6.706
eig_norm2	6.115	0.124	6.244
eigen_pi	0.014	0.003	0.017
g.test	0.006	0.001	0.006
get_presAbs_prots	10.489	0.259	10.754
makeLMFormula	0.001	0.000	0.001
make_intencities	0.009	0.002	0.013
make_meta	0.010	0.003	0.014
peptideLevel_DE	8.514	0.159	8.678
peptideLevel_PresAbsDE	10.395	0.216	10.618
plot_3_pep_trends_NOfile	5.685	0.102	5.791
plot_volcano	8.349	0.173	8.527
plot_volcano_wLab	9.276	0.146	9.427
prot_level_multiMat_PresAbs	14.618	0.238	14.866
prot_level_multi_part	43.817	0.376	44.209
subset_proteins	14.087	0.283	14.376