Package: ProteoMM

Version: 1.0.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ProteoMM_1.0.1.tar.gz

StartedAt: 2019-04-16 02:14:51 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:16:46 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 114.7 seconds

RetCode: 0

Status:  OK

CheckDir: ProteoMM.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ProteoMM_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ProteoMM.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.1’
* 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       26.452  0.004  26.490
subset_proteins              9.192  0.012   9.219
prot_level_multiMat_PresAbs  7.344  0.004   7.355
peptideLevel_PresAbsDE       6.908  0.000   6.937
plot_volcano_wLab            5.852  0.000   5.859
peptideLevel_DE              5.752  0.008   5.776
get_presAbs_prots            5.160  0.004   5.186
* 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-3.8-bioc/meat/ProteoMM.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ProteoMM
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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	3.984	0.032	4.020
convert_log2	0.008	0.000	0.005
eig_norm1	3.260	0.016	3.285
eig_norm2	3.644	0.000	3.681
eigen_pi	0.004	0.004	0.010
g.test	0.000	0.000	0.003
get_presAbs_prots	5.160	0.004	5.186
makeLMFormula	0	0	0
make_intencities	0.004	0.000	0.004
make_meta	0.008	0.000	0.005
peptideLevel_DE	5.752	0.008	5.776
peptideLevel_PresAbsDE	6.908	0.000	6.937
plot_3_pep_trends_NOfile	3.300	0.004	3.315
plot_volcano	4.500	0.000	4.502
plot_volcano_wLab	5.852	0.000	5.859
prot_level_multiMat_PresAbs	7.344	0.004	7.355
prot_level_multi_part	26.452	0.004	26.490
subset_proteins	9.192	0.012	9.219