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BioC 3.0: CHECK report for scsR on oaxaca

This page was generated on 2015-04-10 10:08:40 -0700 (Fri, 10 Apr 2015).

Package 805/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scsR 1.3.2
Andrea Franceschini , Roger Meier , Christian von Mering
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/scsR
Last Changed Rev: 97848 / Revision: 102249
Last Changed Date: 2014-12-22 07:04:14 -0800 (Mon, 22 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: scsR
Version: 1.3.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch scsR_1.3.2.tar.gz
StartedAt: 2015-04-10 03:15:12 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:19:37 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 265.5 seconds
RetCode: 0
Status:  OK 
CheckDir: scsR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch scsR_1.3.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/scsR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scsR’ version ‘1.3.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘STRINGdb’ ‘BiocGenerics’ ‘Biostrings’ ‘IRanges’ ‘plyr’ ‘tcltk’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘scsR’ can be installed ... [19s/24s] 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
* 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 ... NOTE
enrichment_heatmap: no visible global function definition for
  ‘heatmap.2’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [64s/72s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 26.944  1.317  35.201
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/scsR.Rcheck/00check.log’
for details.

scsR.Rcheck/00install.out:

* installing *source* package ‘scsR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scsR)

scsR.Rcheck/scsR-Ex.timings:

nameusersystemelapsed
add_rank_col0.5820.0250.619
add_seed0.2690.0070.279
benchmark_shared_hits3.5630.1374.120
bydf0.4940.0160.642
check_consistency2.3580.0502.585
compare_sorted_geneSets26.944 1.31735.201
create_sd_matrix0.3870.0170.407
delColDf0.2710.0080.280
delete_undefined_rows0.5510.0210.576
enrichment_geneSet0.5280.0220.550
enrichment_heatmap0.4990.0160.516
get_sd_quant1.3060.0781.389
get_seed_oligos_df1.1480.0561.212
intersectAll0.0020.0000.002
launch_RSA0.6140.0260.660
median_replicates1.1510.0671.225
plot_screen_hits2.5550.1313.152
plot_seeds_methods2.4740.2422.738
randomSortOnVal0.2630.0120.276
randomizeInner0.2630.0120.280
removeSharedOffTargets0.9320.0430.976
renameColDf0.2550.0090.271
replace_non_null_elements0.2640.0080.273
seed_correction0.6080.0280.676
seed_correction_pooled0.6620.0320.883
seed_removal0.5280.0200.550
seeds_analysis2.0080.1152.125
sortInner0.3550.0200.375
split_df0.3390.0110.351
transcribe_seqs0.4430.0190.462