Back to Multiple platform build/check report for BioC 3.9
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for anamiR on celaya2

This page was generated on 2019-10-16 12:58:58 -0400 (Wed, 16 Oct 2019).

Package 51/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anamiR 1.12.0
Ti-Tai Wang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/anamiR
Branch: RELEASE_3_9
Last Commit: 7974d7d
Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: anamiR
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:anamiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings anamiR_1.12.0.tar.gz
StartedAt: 2019-10-16 00:29:45 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:53:03 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 1397.8 seconds
RetCode: 0
Status:  OK 
CheckDir: anamiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:anamiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings anamiR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/anamiR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘anamiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘anamiR’ version ‘1.12.0’
* package encoding: UTF-8
* 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 ‘anamiR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 21.5Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata  19.6Mb
* 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 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
GSEA_ana: no visible binding for global variable ‘msigdb.gs’
Undefined global functions or variables:
  msigdb.gs
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
GSEA_res         17.176  0.747 223.617
enrichment        8.127  2.186 669.972
heat_vis          2.134  0.039   8.178
database_support  1.763  0.046  36.651
miR_converter     0.511  0.026   6.421
* 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-3.9-bioc/meat/anamiR.Rcheck/00check.log’
for details.



Installation output

anamiR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL anamiR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘anamiR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (anamiR)

Tests output


Example timings

anamiR.Rcheck/anamiR-Ex.timings

nameusersystemelapsed
GSEA_ana2.1930.7961.779
GSEA_res 17.176 0.747223.617
database_support 1.763 0.04636.651
differExp_continuous0.4460.0200.466
differExp_discrete0.4550.0170.472
enrichment 8.127 2.186669.972
heat_vis2.1340.0398.178
miR_converter0.5110.0266.421
multi_Differ1.3970.0361.434
negative_cor1.6890.0211.711
normalization0.0230.0110.035