Package: ProteoMM

Version: 1.1.1

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_1.1.1.tar.gz

StartedAt: 2019-04-09 02:52:03 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:54:15 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 132.1 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_1.1.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ProteoMM.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.1.1’
* 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       32.430  0.008  32.443
prot_level_multiMat_PresAbs 11.428  0.004  11.431
get_presAbs_prots            8.164  0.000   8.165
subset_proteins              6.669  0.004   6.673
peptideLevel_DE              6.107  0.000   6.111
plot_volcano_wLab            5.248  0.004   5.259
* 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	4.745	0.040	4.785
convert_log2	0.007	0.002	0.009
eig_norm1	3.798	0.008	3.807
eig_norm2	4.208	0.000	4.210
eigen_pi	0.016	0.000	0.016
g.test	0.005	0.000	0.005
get_presAbs_prots	8.164	0.000	8.165
makeLMFormula	0.001	0.000	0.000
make_intencities	0.005	0.000	0.004
make_meta	0.005	0.000	0.005
peptideLevel_DE	6.107	0.000	6.111
peptideLevel_PresAbsDE	4.964	0.003	4.968
plot_3_pep_trends_NOfile	2.628	0.008	2.636
plot_volcano	3.957	0.008	4.017
plot_volcano_wLab	5.248	0.004	5.259
prot_level_multiMat_PresAbs	11.428	0.004	11.431
prot_level_multi_part	32.430	0.008	32.443
subset_proteins	6.669	0.004	6.673