BioC 3.3: CHECK report for SWATH2stats on windows2.bioconductor.org

Package: SWATH2stats

Version: 1.1.0

Command: rm -rf SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && mkdir SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SWATH2stats.buildbin-libdir SWATH2stats_1.1.0.tar.gz >SWATH2stats.Rcheck\00install.out 2>&1 && cp SWATH2stats.Rcheck\00install.out SWATH2stats-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=SWATH2stats.buildbin-libdir --install="check:SWATH2stats-install.out" --force-multiarch --no-vignettes --timings SWATH2stats_1.1.0.tar.gz

StartedAt: 2015-10-27 06:26:03 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:27:05 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 62.0 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && mkdir SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SWATH2stats.buildbin-libdir SWATH2stats_1.1.0.tar.gz >SWATH2stats.Rcheck\00install.out 2>&1 && cp SWATH2stats.Rcheck\00install.out SWATH2stats-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=SWATH2stats.buildbin-libdir --install="check:SWATH2stats-install.out" --force-multiarch --no-vignettes --timings SWATH2stats_1.1.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/SWATH2stats.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SWATH2stats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SWATH2stats' version '1.1.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'imsbInfer'
* 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 whether package 'SWATH2stats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [10s] OK
** running examples for arch 'x64' ... [10s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [5s]
 [5s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [5s]
 [5s] OK
* 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
  'c:/biocbld/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SWATH2stats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'SWATH2stats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SWATH2stats' as SWATH2stats_1.1.0.zip
* DONE (SWATH2stats)

name	user	system	elapsed
assess_decoy_rate	0.22	0.01	0.23
assess_fdr_byrun	0.53	0.00	0.53
assess_fdr_overall	0.34	0.02	0.36
convert4MSstats	0.66	0.01	0.67
convert4aLFQ	0.52	0.00	0.52
convert4mapDIA	0.57	0.02	0.59
convert4pythonscript	0.27	0.01	0.28
disaggregate	0.47	0.00	0.47
filter_all_peptides	0.27	0.00	0.26
filter_mscore_all	0.34	0.00	0.35
filter_mscore_fdr	0.60	0.00	0.59
filter_on_max_peptides	0.31	0.00	0.31
filter_on_min_peptides	0.36	0.00	0.36
filter_proteotypic_peptides	0.36	0.00	0.36
mscore4assayfdr	1.17	0.00	1.17
mscore4pepfdr	0.52	0.00	0.52
mscore4protfdr	0.35	0.00	0.36
plot.fdr_cube	0.35	0.00	0.34
plot.fdr_table	0.31	0.02	0.33
reduce_OpenSWATH_output	0.25	0.02	0.27
sample_annotation	0.42	0.01	0.43
write_matrix_peptides	0.38	0.00	0.38
write_matrix_proteins	0.28	0.00	0.28

name	user	system	elapsed
assess_decoy_rate	0.28	0.00	0.28
assess_fdr_byrun	0.46	0.00	0.45
assess_fdr_overall	0.35	0.00	0.34
convert4MSstats	0.67	0.00	0.67
convert4aLFQ	0.54	0.03	0.58
convert4mapDIA	0.61	0.00	0.61
convert4pythonscript	0.25	0.00	0.25
disaggregate	0.42	0.00	0.42
filter_all_peptides	0.38	0.00	0.37
filter_mscore_all	0.32	0.00	0.33
filter_mscore_fdr	0.66	0.00	0.66
filter_on_max_peptides	0.36	0.00	0.36
filter_on_min_peptides	0.30	0.00	0.29
filter_proteotypic_peptides	0.22	0.02	0.24
mscore4assayfdr	0.96	0.00	0.97
mscore4pepfdr	0.46	0.00	0.45
mscore4protfdr	0.34	0.00	0.34
plot.fdr_cube	0.31	0.00	0.32
plot.fdr_table	0.30	0.00	0.29
reduce_OpenSWATH_output	0.25	0.00	0.25
sample_annotation	0.25	0.00	0.25
write_matrix_peptides	0.25	0.00	0.25
write_matrix_proteins	0.25	0.00	0.25