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BioC 3.6: CHECK report for isomiRs on veracruz1

This page was generated on 2017-08-16 13:48:37 -0400 (Wed, 16 Aug 2017).

Package 700/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isomiRs 1.5.4
Lorena Pantano
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/isomiRs
Last Changed Rev: 131530 / Revision: 131943
Last Changed Date: 2017-07-24 10:42:37 -0400 (Mon, 24 Jul 2017)
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
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: isomiRs
Version: 1.5.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings isomiRs_1.5.4.tar.gz
StartedAt: 2017-08-16 04:42:50 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:49:02 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 372.0 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_1.5.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.5.4’
* 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 ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
* 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
isoCorrect: warning in gamlss(reads ˜ SampleID + random(miRNA),
  sigma.fo = ˜SampleID + random(miRNA), data = train, family = "LQNO",
  control = gamlss.control(n.cyc = cycles, c.crit = 0.1, mu.step = 1,
  sigma.step = 1), method = RS()): partial argument match of 'sigma.fo'
  to 'sigma.formula'
isoCorrect: warning in gamlss(reads ˜ SampleID + random(miRNA) +
  offset(off.m), sigma.fo = ˜SampleID + random(miRNA) + offset(off.s),
  data = data.LQNO, family = "LQNO", control = gamlss.control(n.cyc =
  cycles, c.crit = 0.1, mu.step = 1, sigma.step = 1, gd.tol = Inf),
  i.control = glim.control(cc = 0.001, cyc = cycles, glm.trace = FALSE,
  bf.cyc = 300, bf.tol = 0.1, bf.trace = FALSE), method = RS()):
  partial argument match of 'sigma.fo' to 'sigma.formula'
.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_all_iso : <anonymous>: no visible binding for global variable
  ‘mism’
.plot_all_iso : <anonymous>: no visible binding for global variable
  ‘add’
.plot_all_iso : <anonymous>: no visible binding for global variable
  ‘t5’
.plot_all_iso : <anonymous>: no visible binding for global variable
  ‘t3’
.plot_all_iso: no visible binding for global variable ‘type’
.plot_all_iso: no visible binding for global variable ‘freq’
.plot_all_iso: no visible binding for global variable ‘condition’
.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’
isoCorrect: no visible global function definition for ‘RS’
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 RS 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   66.055  4.123  72.587
isoDE         5.732  0.162   6.046
isoCorrect    5.271  0.201   5.622
isoPLSDAplot  5.058  0.099   5.354
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.Rcheck/00check.log’
for details.

isomiRs.Rcheck/00install.out:

* installing *source* package ‘isomiRs’ ...
** R
** data
*** moving datasets to lazyload DB
** 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
IsomirDataSeq1.8450.0391.918
IsomirDataSeqFromFiles0.8410.0040.872
counts2.7340.1392.972
design1.1200.0621.216
find_targets0.1170.0010.118
isoCorrect5.2710.2015.622
isoCounts2.4330.1752.666
isoDE5.7320.1626.046
isoNetwork66.055 4.12372.587
isoNorm3.6570.1843.901
isoPLSDA3.5060.2543.896
isoPLSDAplot5.0580.0995.354
isoPlot2.4960.1402.737
isoPlotPosition2.1830.1642.416
isoSelect1.3090.1191.462
isoTop0.9910.0631.069