Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2021-11-27 14:05:25 -0500 (Sat, 27 Nov 2021).

CHECK results for SIMD on riesling1

To the developers/maintainers of the SIMD package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIMD.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 1787/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMD 1.13.0  (landing page)
Jiadi Zhu
Snapshot Date: 2021-11-26 14:50:14 -0500 (Fri, 26 Nov 2021)
git_url: https://git.bioconductor.org/packages/SIMD
git_branch: master
git_last_commit: 84a8f65
git_last_commit_date: 2021-10-26 12:46:50 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SIMD
Version: 1.13.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMD.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SIMD_1.13.0.tar.gz
StartedAt: 2021-11-27 04:04:33 -0500 (Sat, 27 Nov 2021)
EndedAt: 2021-11-27 04:10:07 -0500 (Sat, 27 Nov 2021)
EllapsedTime: 333.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SIMD.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMD.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SIMD_1.13.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/SIMD.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SIMD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIMD' version '1.13.0'
* 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 'SIMD' 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
* 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 LazyData ... 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/SIMD/libs/x64/SIMD.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 ... 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
  'D:/biocbuild/bbs-3.15-bioc/meat/SIMD.Rcheck/00check.log'
for details.



Installation output

SIMD.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/SIMD_1.13.0.tar.gz && rm -rf SIMD.buildbin-libdir && mkdir SIMD.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIMD.buildbin-libdir SIMD_1.13.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SIMD_1.13.0.zip && rm SIMD_1.13.0.tar.gz SIMD_1.13.0.zip
###
##############################################################################
##############################################################################


  % 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 92501  100 92501    0     0   190k      0 --:--:-- --:--:-- --:--:--  190k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'SIMD' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c pvalueclassify.c -o pvalueclassify.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o SIMD.dll tmp.def init.o pvalueclassify.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/SIMD.buildbin-libdir/00LOCK-SIMD/00new/SIMD/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SIMD'
    finding HTML links ... done
    EM2_H1ESB1_MeDIP_sigleCpG               html  
    EM2_H1ESB2_MeDIP_sigleCpG               html  
    EM_H1ESB1_MeDIP_sigleCpG                html  
    EMalgorithm                             html  
    EMtest                                  html  
    H1ESB1_MRE_sigleCpG                     html  
    H1ESB2_MRE_sigleCpG                     html  
    SIMD-package                            html  
    all_CpGsite_bin_chr18                   html  
    classifypvalue                          html  
    emalgth                                 html  
    emalgth1                                html  
    probBinom                               html  
    three_mre_cpg                           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
* MD5 sums
packaged installation of 'SIMD' as SIMD_1.13.0.zip
* DONE (SIMD)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'SIMD' successfully unpacked and MD5 sums checked

Tests output


Example timings

SIMD.Rcheck/SIMD-Ex.timings

nameusersystemelapsed
EMalgorithm1.860.101.95
EMtest0.350.010.36
emalgth000
emalgth10.010.000.01
probBinom0.000.020.02