Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-25 14:06:05 -0400 (Mon, 25 Oct 2021).

CHECK results for BAC on riesling1

To the developers/maintainers of the BAC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BAC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 104/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BAC 1.53.0  (landing page)
Raphael Gottardo
Snapshot Date: 2021-10-24 14:50:04 -0400 (Sun, 24 Oct 2021)
git_url: https://git.bioconductor.org/packages/BAC
git_branch: master
git_last_commit: c132ac8
git_last_commit_date: 2021-05-19 11:40:12 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: BAC
Version: 1.53.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BAC.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BAC_1.53.0.tar.gz
StartedAt: 2021-10-24 23:58:46 -0400 (Sun, 24 Oct 2021)
EndedAt: 2021-10-25 00:01:49 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 182.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BAC.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BAC.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BAC_1.53.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/BAC.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BAC' version '1.53.0'
* 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 'BAC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
BAC: no visible global function definition for 'median'
BAC: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median
Consider adding
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: BAC.Rd:37-38: Dropping empty section \note
prepare_Rd: CallRegions.Rd:21-23: Dropping empty section \details
prepare_Rd: CallRegions.Rd:34-35: Dropping empty section \note
* 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 'D:/biocbuild/bbs-3.14-bioc/R/library/BAC/libs/i386/BAC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/BAC/libs/x64/BAC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
CallRegions 36.33   0.01   36.34
BAC         36.25   0.00   36.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
BAC         31.32      0   31.32
CallRegions 31.29      0   31.29
* 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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/BAC.Rcheck/00check.log'
for details.



Installation output

BAC.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BAC_1.53.0.tar.gz && rm -rf BAC.buildbin-libdir && mkdir BAC.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BAC.buildbin-libdir BAC_1.53.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BAC_1.53.0.zip && rm BAC_1.53.0.tar.gz BAC_1.53.0.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
 11  828k   11 95639    0     0   499k      0  0:00:01 --:--:--  0:00:01  499k
100  828k  100  828k    0     0  1137k      0 --:--:-- --:--:-- --:--:-- 1135k

install for i386

* installing *source* package 'BAC' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c BAC.c -o BAC.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c util.c -o util.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o BAC.dll tmp.def BAC.o util.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/BAC.buildbin-libdir/00LOCK-BAC/00new/BAC/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BAC'
    finding HTML links ... done
    BAC                                     html  
    CallRegions                             html  
    ER                                      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 'BAC' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c BAC.c -o BAC.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c util.c -o util.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o BAC.dll tmp.def BAC.o util.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/BAC.buildbin-libdir/BAC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BAC' as BAC_1.53.0.zip
* DONE (BAC)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BAC' successfully unpacked and MD5 sums checked

Tests output


Example timings

BAC.Rcheck/examples_i386/BAC-Ex.timings

nameusersystemelapsed
BAC36.25 0.0036.25
CallRegions36.33 0.0136.34

BAC.Rcheck/examples_x64/BAC-Ex.timings

nameusersystemelapsed
BAC31.32 0.0031.32
CallRegions31.29 0.0031.29