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CHECK report for microRNA on tokay2

This page was generated on 2019-04-09 11:56:40 -0400 (Tue, 09 Apr 2019).

Package 980/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microRNA 1.41.0
"James F. Reid"
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/microRNA
Branch: master
Last Commit: c211564
Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: microRNA
Version: 1.41.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microRNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings microRNA_1.41.0.tar.gz
StartedAt: 2019-04-09 04:15:06 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:17:11 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 124.7 seconds
RetCode: 0
Status:  OK  
CheckDir: microRNA.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:microRNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings microRNA_1.41.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/microRNA.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'microRNA/DESCRIPTION' ... OK
* this is package 'microRNA' version '1.41.0'
* 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 'microRNA' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      5.4Mb
    extdata   2.0Mb
    libs      1.0Mb
* checking package 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/microRNA/libs/i386/microRNA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/microRNA/libs/x64/microRNA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
matchSeeds 4.91   0.18    5.08
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/microRNA.Rcheck/00check.log'
for details.



Installation output

microRNA.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/microRNA_1.41.0.tar.gz && rm -rf microRNA.buildbin-libdir && mkdir microRNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microRNA.buildbin-libdir microRNA_1.41.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL microRNA_1.41.0.zip && rm microRNA_1.41.0.tar.gz microRNA_1.41.0.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 5884k  100 5884k    0     0  47.2M      0 --:--:-- --:--:-- --:--:-- 49.9M

install for i386

* installing *source* package 'microRNA' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c longest_common_substring.cpp -o longest_common_substring.o
longest_common_substring.cpp: In function 'SEXPREC* longest_common_substring(SEXP)':
longest_common_substring.cpp:55:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i == len[index] - 1) { // ignore null termination character
               ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o microRNA.dll tmp.def longest_common_substring.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/microRNA.buildbin-libdir/00LOCK-microRNA/00new/microRNA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'microRNA'
    finding HTML links ... done
    RNA2DNA                                 html  
    get_selfhyb_subseq                      html  
    hsSeqs                                  html  
    hsTargets                               html  
    matchSeeds                              html  
    mmSeqs                                  html  
    mmTargets                               html  
    s3utr                                   html  
    seedRegions                             html  
** building package indices
** 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 'microRNA' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c longest_common_substring.cpp -o longest_common_substring.o
longest_common_substring.cpp: In function 'SEXPREC* longest_common_substring(SEXP)':
longest_common_substring.cpp:55:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i == len[index] - 1) { // ignore null termination character
               ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o microRNA.dll tmp.def longest_common_substring.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/microRNA.buildbin-libdir/microRNA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'microRNA' as microRNA_1.41.0.zip
* DONE (microRNA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'microRNA' successfully unpacked and MD5 sums checked

Tests output


Example timings

microRNA.Rcheck/examples_i386/microRNA-Ex.timings

nameusersystemelapsed
RNA2DNA000
get_selfhyb_subseq0.030.000.12
hsSeqs0.030.000.03
hsTargets0.620.060.69
matchSeeds4.910.185.08
mmSeqs000
mmTargets1.620.311.93
s3utr000
seedRegions0.020.000.02

microRNA.Rcheck/examples_x64/microRNA-Ex.timings

nameusersystemelapsed
RNA2DNA000
get_selfhyb_subseq0.030.000.04
hsSeqs0.020.000.02
hsTargets0.330.040.37
matchSeeds4.400.134.53
mmSeqs0.020.000.02
mmTargets2.130.032.16
s3utr000
seedRegions0.010.000.01