Package: ProteoMM

Version: 1.2.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ProteoMM_1.2.0.tar.gz

StartedAt: 2019-10-16 04:07:41 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:09:57 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 135.9 seconds

RetCode: 0

Status:  OK

CheckDir: ProteoMM.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ProteoMM_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ProteoMM.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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       28.327  0.004  28.331
prot_level_multiMat_PresAbs 10.728  0.000  10.733
subset_proteins              9.418  0.004   9.423
peptideLevel_PresAbsDE       7.960  0.000   7.961
peptideLevel_DE              6.623  0.007   6.635
get_presAbs_prots            6.468  0.012   6.479
plot_volcano_wLab            6.431  0.004   6.436
MBimpute                     5.451  0.028   5.483
plot_volcano                 5.187  0.004   5.193
* 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-3.9-bioc/meat/ProteoMM.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ProteoMM
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* installing to library ‘/home/biocbuild/bbs-3.9-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	5.451	0.028	5.483
convert_log2	0.009	0.000	0.009
eig_norm1	4.688	0.004	4.694
eig_norm2	3.312	0.003	3.315
eigen_pi	0.016	0.000	0.016
g.test	0.005	0.000	0.006
get_presAbs_prots	6.468	0.012	6.479
makeLMFormula	0.000	0.000	0.001
make_intencities	0.005	0.000	0.005
make_meta	0.005	0.000	0.006
peptideLevel_DE	6.623	0.007	6.635
peptideLevel_PresAbsDE	7.960	0.000	7.961
plot_3_pep_trends_NOfile	3.969	0.000	3.969
plot_volcano	5.187	0.004	5.193
plot_volcano_wLab	6.431	0.004	6.436
prot_level_multiMat_PresAbs	10.728	0.000	10.733
prot_level_multi_part	28.327	0.004	28.331
subset_proteins	9.418	0.004	9.423