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 | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings isomiRs_1.4.0.tar.gz
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* 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.