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BioC 3.0: CHECK report for scsR on perceval

This page was generated on 2015-04-10 09:59:21 -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 06:12:33 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 06:17:54 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 321.2 seconds
RetCode: 0
Status:  OK 
CheckDir: scsR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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-darwin10.8.0 (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 ... [26s/28s] 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 ... [75s/75s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 30.556  1.578  32.325
benchmark_shared_hits    5.077  0.244   5.315
* 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_col0.8330.0550.888
add_seed0.2360.0100.246
benchmark_shared_hits5.0770.2445.315
bydf0.5240.0250.551
check_consistency2.8200.0892.929
compare_sorted_geneSets30.556 1.57832.325
create_sd_matrix0.3860.0250.412
delColDf0.2440.0110.255
delete_undefined_rows0.5600.0370.601
enrichment_geneSet0.5090.0420.554
enrichment_heatmap0.4570.0210.479
get_sd_quant1.4780.1111.604
get_seed_oligos_df1.1630.0791.241
intersectAll0.0040.0000.004
launch_RSA0.6270.0410.667
median_replicates1.1370.1111.462
plot_screen_hits2.5040.1862.688
plot_seeds_methods3.2520.4153.620
randomSortOnVal0.2490.0170.265
randomizeInner0.2320.0100.242
removeSharedOffTargets1.0370.0441.074
renameColDf0.2470.0320.279
replace_non_null_elements0.2440.0240.268
seed_correction0.6530.0550.698
seed_correction_pooled0.7130.0600.762
seed_removal0.5730.0440.612
seeds_analysis2.2740.1822.442
sortInner0.4160.0490.528
split_df0.3150.0270.371
transcribe_seqs0.4400.0350.546