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BioC 3.4: CHECK report for isomiRs on malbec1

This page was generated on 2017-04-15 16:13:43 -0400 (Sat, 15 Apr 2017).

Package 650/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isomiRs 1.2.0
Lorena Pantano
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/isomiRs
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: isomiRs
Version: 1.2.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings isomiRs_1.2.0.tar.gz
StartedAt: 2017-04-14 23:24:27 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:28:37 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 249.2 seconds
RetCode: 0
Status:  OK 
CheckDir: isomiRs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings isomiRs_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/isomiRs.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ‘subs’
.clean_low_rate_changes: no visible binding for global variable ‘mir’
.clean_low_rate_changes: no visible binding for global variable ‘freq’
.clean_low_rate_changes: no visible binding for global variable
  ‘total_subs’
.clean_low_rate_changes: no visible binding for global variable
  ‘total_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
  ‘ambiguity’
.filter_by_cov: no visible binding for global variable ‘subs’
.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’
isoNetwork: no visible global function definition for ‘n’
isoPLSDAplot: no visible binding for global variable ‘condition’
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 global function definition for ‘n’
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 global function definition for ‘n’
isoSelect.IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘mir’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
  variable ‘mir’
Undefined global functions or variables:
  Count DB X1 X2 add ambiguity average change condition current
  enrichGO error freq gene go group mir n ngene reference rowMax rowMin
  sel_genes subs t3 t5 term term_short total_mir total_subs 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 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 49.492   1.18  50.742
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-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
IsomirDataSeq0.1800.0160.194
IsomirDataSeqFromFiles0.1160.0000.117
counts2.5520.0362.586
find_targets0.0760.0040.082
isoCounts3.4320.0043.436
isoDE2.9520.0282.979
isoNetwork49.492 1.18050.742
isoNorm2.4480.0002.446
isoPLSDA1.9240.0001.926
isoPLSDAplot3.4480.0283.476
isoPlot1.7440.0001.743
isoPlotPosition1.8360.0041.842
isoSelect1.5120.0281.540
isoTop1.4680.0121.481