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BioC 3.1: CHECK report for scsR on zin2

This page was generated on 2015-10-09 09:25:57 -0700 (Fri, 09 Oct 2015).

Package 882/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scsR 1.4.0
Andrea Franceschini , Roger Meier , Christian von Mering
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/scsR
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scsR
Version: 1.4.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.4.0.tar.gz
StartedAt: 2015-10-09 05:21:15 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:23:17 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 121.5 seconds
RetCode: 0
Status:  OK 
CheckDir: scsR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/scsR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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 ... [8s/8s] 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 ... [37s/36s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 14.925  0.319   15.16
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/scsR.Rcheck/00check.log’
for details.


scsR.Rcheck/00install.out:

* installing *source* package ‘scsR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (scsR)

scsR.Rcheck/scsR-Ex.timings:

nameusersystemelapsed
add_rank_col0.2900.0120.315
add_seed0.1900.0040.193
benchmark_shared_hits2.3070.0412.345
bydf0.3540.0040.357
check_consistency1.5280.0121.538
compare_sorted_geneSets14.925 0.31915.160
create_sd_matrix0.2760.0040.279
delColDf0.2020.0000.201
delete_undefined_rows0.4510.0000.451
enrichment_geneSet0.4050.0000.405
enrichment_heatmap0.3570.0000.357
get_sd_quant1.0090.0151.019
get_seed_oligos_df0.6710.0170.682
intersectAll0.0010.0000.002
launch_RSA0.3530.0080.359
median_replicates0.6660.0160.687
plot_screen_hits1.3470.0361.372
plot_seeds_methods1.6370.0891.701
randomSortOnVal0.1930.0000.200
randomizeInner0.1920.0040.196
removeSharedOffTargets0.6810.0120.691
renameColDf0.1930.0000.193
replace_non_null_elements0.1960.0000.196
seed_correction0.4100.0080.416
seed_correction_pooled0.4130.0040.414
seed_removal0.3590.0080.365
seeds_analysis1.3280.0171.335
sortInner0.2400.0080.247
split_df0.2470.0000.247
transcribe_seqs0.2690.0000.268