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BioC 3.4: CHECK report for scsR on zin1

This page was generated on 2016-09-21 03:38:49 -0700 (Wed, 21 Sep 2016).

Package 1089/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scsR 1.9.0
Andrea Franceschini , Roger Meier , Christian von Mering
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/scsR
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: 1.9.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.9.0.tar.gz
StartedAt: 2016-09-20 12:21:08 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:22:57 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 109.8 seconds
RetCode: 0
Status:  OK 
CheckDir: scsR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/scsR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.9.0’
* 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 ... 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
OPIrsaScore : <anonymous>: no visible global function definition for
  ‘phyper’
enrichment_geneSet: no visible global function definition for ‘phyper’
enrichment_heatmap: no visible global function definition for
  ‘heatmap.2’
get_seed_oligos_df: no visible global function definition for
  ‘txtProgressBar’
get_seed_oligos_df: no visible global function definition for
  ‘setTxtProgressBar’
get_seed_oligos_df: no visible global function definition for ‘phyper’
get_seed_oligos_df: no visible global function definition for ‘ks.test’
plot_seed_score_sd: no visible global function definition for ‘lm’
plot_seed_score_sd: no visible global function definition for
  ‘cor.test’
seed_correction: no visible global function definition for
  ‘txtProgressBar’
seed_correction: no visible global function definition for
  ‘setTxtProgressBar’
seed_correction_pooled: no visible global function definition for
  ‘txtProgressBar’
seed_correction_pooled: no visible global function definition for
  ‘setTxtProgressBar’
seed_removal: no visible global function definition for
  ‘txtProgressBar’
seed_removal: no visible global function definition for
  ‘setTxtProgressBar’
seeds_analysis : <anonymous>: no visible global function definition for
  ‘ks.test’
seeds_analysis: no visible global function definition for ‘phyper’
transcribe_seqs: no visible global function definition for
  ‘txtProgressBar’
transcribe_seqs: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  cor.test heatmap.2 ks.test lm phyper setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "cor.test", "ks.test", "lm", "phyper")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 14.368  0.268  14.906
* 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-3.4-bioc/meat/scsR.Rcheck/00check.log’
for details.


scsR.Rcheck/00install.out:

* installing *source* package ‘scsR’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
* DONE (scsR)

scsR.Rcheck/scsR-Ex.timings:

nameusersystemelapsed
add_rank_col0.3440.0080.349
add_seed0.3440.0000.347
benchmark_shared_hits2.0400.0602.094
bydf0.3480.0040.351
check_consistency1.4280.0121.441
compare_sorted_geneSets14.368 0.26814.906
create_sd_matrix0.3400.0280.368
delColDf0.2120.0040.214
delete_undefined_rows0.3840.0000.385
enrichment_geneSet0.4240.0080.450
enrichment_heatmap0.3640.0160.390
get_sd_quant1.0120.0241.062
get_seed_oligos_df0.6680.0280.706
intersectAll0.0000.0000.001
launch_RSA0.3640.0080.368
median_replicates0.7320.0320.766
plot_screen_hits1.3320.0281.361
plot_seeds_methods1.7600.0601.851
randomSortOnVal0.1880.0080.194
randomizeInner0.1920.0080.200
removeSharedOffTargets0.7000.0360.734
renameColDf0.1880.0080.198
replace_non_null_elements0.1960.0040.197
seed_correction0.4840.0080.489
seed_correction_pooled0.4360.0040.441
seed_removal0.400.000.42
seeds_analysis1.2320.0361.271
sortInner0.2640.0040.267
split_df0.2320.0040.236
transcribe_seqs0.3000.0080.307