Package: ProteoMM

Version: 1.4.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ProteoMM_1.4.0.tar.gz

StartedAt: 2020-04-15 06:06:26 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:08:44 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 138.8 seconds

RetCode: 0

Status:  OK

CheckDir: ProteoMM.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ProteoMM_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ProteoMM.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProteoMM/DESCRIPTION’ ... OK
* this is package ‘ProteoMM’ version ‘1.4.0’
* 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       30.680  0.016  30.778
prot_level_multiMat_PresAbs 10.568  0.004  10.594
subset_proteins             10.156  0.012  10.197
get_presAbs_prots            7.128  0.008   7.155
plot_volcano                 6.320  0.012   6.345
peptideLevel_PresAbsDE       6.232  0.012   6.280
MBimpute                     5.936  0.044   6.080
plot_volcano_wLab            5.728  0.000   5.735
peptideLevel_DE              5.600  0.008   5.638
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/ProteoMM.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ProteoMM
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	5.936	0.044	6.080
convert_log2	0.004	0.000	0.005
eig_norm1	3.660	0.004	3.668
eig_norm2	4.224	0.000	4.258
eigen_pi	0.012	0.000	0.015
g.test	0.004	0.000	0.005
get_presAbs_prots	7.128	0.008	7.155
makeLMFormula	0	0	0
make_intencities	0.004	0.000	0.004
make_meta	0.004	0.000	0.004
peptideLevel_DE	5.600	0.008	5.638
peptideLevel_PresAbsDE	6.232	0.012	6.280
plot_3_pep_trends_NOfile	3.920	0.004	3.930
plot_volcano	6.320	0.012	6.345
plot_volcano_wLab	5.728	0.000	5.735
prot_level_multiMat_PresAbs	10.568	0.004	10.594
prot_level_multi_part	30.680	0.016	30.778
subset_proteins	10.156	0.012	10.197