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BioC 3.5: CHECK report for isomiRs on veracruz2

This page was generated on 2017-08-16 13:34:29 -0400 (Wed, 16 Aug 2017).

Package 690/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isomiRs 1.4.0
Lorena Pantano
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/isomiRs
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: isomiRs
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings isomiRs_1.4.0.tar.gz
StartedAt: 2017-08-16 04:27:05 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:32:58 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 353.7 seconds
RetCode: 0
Status:  OK 
CheckDir: isomiRs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings isomiRs_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/isomiRs.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isomiRs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘isomiRs’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘isomiRs’ 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
.apply_median: no visible global function definition for ‘rowMax’
.apply_median: no visible global function definition for ‘rowMin’
.clean_low_rate_changes: no visible binding for global variable ‘mism’
.clean_low_rate_changes: no visible binding for global variable
  ‘ambiguity’
.clean_low_rate_changes: no visible binding for global variable ‘af’
.clean_low_rate_changes: no visible binding for global variable ‘mir’
.clean_low_rate_changes: no visible binding for global variable ‘add’
.clean_low_rate_changes: no visible binding for global variable ‘t5’
.clean_low_rate_changes: no visible binding for global variable ‘t3’
.clean_low_rate_changes: no visible binding for global variable ‘DB’
.clean_low_rate_changes: no visible binding for global variable ‘freq’
.filter_by_cov: no visible binding for global variable ‘DB’
.filter_by_cov: no visible binding for global variable ‘add’
.filter_by_cov: no visible binding for global variable ‘mism’
.filter_by_cov: no visible binding for global variable ‘mism_n’
.filter_by_cov: no visible binding for global variable ‘mir_n’
.filter_by_cov: no visible binding for global variable ‘mism_f’
.filter_by_cov: no visible binding for global variable ‘mir_f’
.filter_by_cov: no visible binding for global variable ‘af’
.filter_by_cov: no visible binding for global variable ‘enrich’
.filter_by_cov: no visible binding for global variable ‘id’
.plot_profiles : <anonymous>: no visible binding for global variable
  ‘group’
.plot_profiles : <anonymous>: no visible binding for global variable
  ‘average’
.run_enricher: no visible binding for global variable ‘sel_genes’
.run_enricher: no visible global function definition for ‘enrichGO’
.run_enricher: no visible binding for global variable ‘Count’
.viz_mirna_gene_enrichment: no visible binding for global variable ‘X1’
.viz_mirna_gene_enrichment: no visible binding for global variable ‘X2’
.viz_mirna_gene_enrichment: no visible binding for global variable
  ‘value’
.viz_mirna_gene_enrichment: no visible binding for global variable
  ‘type’
from_pairs_to_matrix: no visible global function definition for ‘error’
from_pairs_to_matrix: no visible binding for global variable ‘gene’
from_pairs_to_matrix: no visible binding for global variable ‘mir’
from_pairs_to_matrix: no visible binding for global variable ‘value’
isoNetwork : <anonymous>: no visible binding for global variable
  ‘value’
isoNetwork : <anonymous>: no visible binding for global variable ‘X1’
isoNetwork : <anonymous>: no visible binding for global variable ‘X2’
isoNetwork: no visible binding for global variable ‘mir’
isoNetwork: no visible binding for global variable ‘go’
isoPLSDAplot: no visible binding for global variable ‘condition’
isoPlot: no visible binding for global variable ‘pct_abundance’
isoPlotNet: no visible binding for global variable ‘term’
isoPlotNet: no visible binding for global variable ‘group’
isoPlotNet: no visible binding for global variable ‘ngene’
isoPlotNet: no visible binding for global variable ‘term_short’
isoPlotNet: no visible binding for global variable ‘mir’
isoPlotNet: no visible binding for global variable ‘value’
isoPlotNet : <anonymous>: no visible binding for global variable ‘y’
isoPlotPosition: no visible binding for global variable ‘reference’
isoPlotPosition: no visible binding for global variable ‘current’
isoPlotPosition: no visible binding for global variable ‘change’
isoPlotPosition: no visible binding for global variable ‘pct_abundance’
isoSelect.IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘mir’
isoSelect.IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘mism’
isoSelect.IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘add’
isoSelect.IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘t5’
isoSelect.IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘t3’
isoSelect.IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘id’
isoSelect.IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘freq’
isoSelect.IsomirDataSeq: no visible binding for global variable ‘freq’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘mir’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘mism’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘add’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘t5’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘t3’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘id’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘freq’
isoSelect,IsomirDataSeq: no visible binding for global variable ‘freq’
Undefined global functions or variables:
  Count DB X1 X2 add af ambiguity average change condition current
  enrich enrichGO error freq gene go group id mir mir_f mir_n mism
  mism_f mism_n ngene pct_abundance reference rowMax rowMin sel_genes
  t3 t5 term term_short type value y
* 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
isoNetwork   65.382  3.874  71.314
isoDE         6.741  0.101   7.046
isoPLSDAplot  6.579  0.195   6.980
isoNorm       4.940  0.139   5.233
isoPLSDA      4.875  0.204   5.216
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/isomiRs.Rcheck/00check.log’
for details.


isomiRs.Rcheck/00install.out:

* installing *source* package ‘isomiRs’ ...
** 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 (isomiRs)

isomiRs.Rcheck/isomiRs-Ex.timings:

nameusersystemelapsed
IsomirDataSeq1.6190.0421.704
IsomirDataSeqFromFiles0.6770.0040.710
counts3.6050.0803.829
design2.5630.0472.671
find_targets0.1440.0010.148
isoCounts4.3120.0674.484
isoDE6.7410.1017.046
isoNetwork65.382 3.87471.314
isoNorm4.9400.1395.233
isoPLSDA4.8750.2045.216
isoPLSDAplot6.5790.1956.980
isoPlot3.4720.0613.642
isoPlotPosition2.9340.0403.072
isoSelect2.6160.0382.747
isoTop2.3270.0462.458