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CHECK report for anamiR on tokay2

This page was generated on 2019-10-16 12:37:04 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:anamiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings anamiR_1.12.0.tar.gz
StartedAt: 2019-10-16 01:53:57 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:33:38 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 2380.6 seconds
RetCode: 0
Status:  OK  
CheckDir: anamiR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:anamiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings anamiR_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/anamiR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'anamiR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 21.6Mb
  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
* 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
* 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
GSEA_res         9.20   0.58  211.88
enrichment       5.23   0.61  689.41
heat_vis         1.82   0.14    7.10
GSEA_ana         1.45   0.12   17.45
database_support 1.19   0.03   40.10
miR_converter    0.32   0.00    5.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
GSEA_res         11.30   0.39  219.17
enrichment        7.05   0.75  686.54
database_support  1.80   0.03   33.27
heat_vis          1.58   0.11    7.47
miR_converter     0.19   0.02    5.53
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/anamiR.Rcheck/00check.log'
for details.



Installation output

anamiR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/anamiR_1.12.0.tar.gz && rm -rf anamiR.buildbin-libdir && mkdir anamiR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=anamiR.buildbin-libdir anamiR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL anamiR_1.12.0.zip && rm anamiR_1.12.0.tar.gz anamiR_1.12.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 10.4M  100 10.4M    0     0  62.6M      0 --:--:-- --:--:-- --:--:-- 65.4M

install for i386

* 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
  converting help for package 'anamiR'
    finding HTML links ... done
    GSEA_ana                                html  
    GSEA_res                                html  
    anamiR                                  html  
    database_support                        html  
    differExp_continuous                    html  
    differExp_discrete                      html  
    egSymb                                  html  
    enrichment                              html  
    heat_vis                                html  
    miR_converter                           html  
    mirna                                   html  
    mrna                                    html  
    msigdb.gs                               html  
    multi_Differ                            html  
    negative_cor                            html  
    normalization                           html  
    pheno.mirna                             html  
    pheno.mrna                              html  
    table_pre                               html  
** 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

install for x64

* installing *source* package 'anamiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'anamiR' as anamiR_1.12.0.zip
* DONE (anamiR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'anamiR' successfully unpacked and MD5 sums checked

Tests output


Example timings

anamiR.Rcheck/examples_i386/anamiR-Ex.timings

nameusersystemelapsed
GSEA_ana 1.45 0.1217.45
GSEA_res 9.20 0.58211.88
database_support 1.19 0.0340.10
differExp_continuous0.290.020.31
differExp_discrete0.220.010.23
enrichment 5.23 0.61689.41
heat_vis1.820.147.10
miR_converter0.320.005.35
multi_Differ0.780.020.80
negative_cor0.780.000.78
normalization0.020.000.02

anamiR.Rcheck/examples_x64/anamiR-Ex.timings

nameusersystemelapsed
GSEA_ana2.000.031.95
GSEA_res 11.30 0.39219.17
database_support 1.80 0.0333.27
differExp_continuous0.310.030.34
differExp_discrete0.240.000.24
enrichment 7.05 0.75686.54
heat_vis1.580.117.47
miR_converter0.190.025.53
multi_Differ1.170.031.20
negative_cor0.950.000.96
normalization0.020.000.01