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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### rm -rf isomiRs.buildbin-libdir isomiRs.Rcheck && mkdir isomiRs.buildbin-libdir isomiRs.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isomiRs.buildbin-libdir isomiRs_1.4.0.tar.gz >isomiRs.Rcheck\00install.out 2>&1 && cp isomiRs.Rcheck\00install.out isomiRs-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=isomiRs.buildbin-libdir --install="check:isomiRs-install.out" --force-multiarch --no-vignettes --timings isomiRs_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/isomiRs.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
isoNetwork 66.99 4.37 77.83
isoDE 6.45 0.11 6.56
isoPLSDAplot 5.69 0.03 5.72
counts 5.04 0.24 5.26
isoCounts 5.17 0.07 5.24
isoPLSDA 4.56 0.61 5.17
isoNorm 4.98 0.05 5.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
isoNetwork 62.49 2.92 65.43
isoDE 5.87 0.02 5.89
isoPLSDAplot 5.78 0.04 5.86
isoPlot 5.38 0.02 5.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.5-bioc/meat/isomiRs.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'isomiRs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'isomiRs' as isomiRs_1.4.0.zip
* DONE (isomiRs)