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CHECK report for HEM on tokay1

This page was generated on 2021-01-19 11:55:30 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE HEM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 825/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HEM 1.62.0
HyungJun Cho
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/HEM
Branch: RELEASE_3_12
Last Commit: 9f7f3a0
Last Changed Date: 2020-10-27 10:24:21 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HEM
Version: 1.62.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings HEM_1.62.0.tar.gz
StartedAt: 2021-01-19 03:47:58 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 03:49:06 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 67.8 seconds
RetCode: 0
Status:  OK  
CheckDir: HEM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings HEM_1.62.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/HEM.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HEM/DESCRIPTION' ... OK
* this is package 'HEM' version '1.62.0'
* 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 'HEM' 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* 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-3.12-bioc/R/library/HEM/libs/i386/HEM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'putchar', possibly from 'putchar' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/HEM/libs/x64/HEM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'putchar', possibly from 'putchar' (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
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/HEM.Rcheck/00check.log'
for details.



Installation output

HEM.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/HEM_1.62.0.tar.gz && rm -rf HEM.buildbin-libdir && mkdir HEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HEM.buildbin-libdir HEM_1.62.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL HEM_1.62.0.zip && rm HEM_1.62.0.tar.gz HEM_1.62.0.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  342k  100  342k    0     0  12.5M      0 --:--:-- --:--:-- --:--:-- 14.5M

install for i386

* installing *source* package 'HEM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hem.c -o hem.o
hem.c: In function 'onelayerhem':
hem.c:1390:12: warning: variable 'k' set but not used [-Wunused-but-set-variable]
  int i, j, k, m, n;
            ^
hem.c: In function 'chk_prt':
hem.c:1593:16: warning: variable 'l' set but not used [-Wunused-but-set-variable]
   int i, j, k, l;
                ^
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o HEM.dll tmp.def hem.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/HEM.buildbin-libdir/00LOCK-HEM/00new/HEM/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HEM'
    finding HTML links ... done
    am.tran                                 html  
    am.tran.half                            html  
    base.ASE.Olig                           html  
    base.PSE.Olig                           html  
    base.error.Olig                         html  
    base.error.Olig.quanOnly                html  
    boot.base.ASE.Olig                      html  
    boot.base.PSE.Olig                      html  
    boot.base.error.Olig                    html  
    fixbound.predict.smooth.spline          html  
    hem                                     html  
    hem.eb.prior                            html  
    hem.fdr                                 html  
    hem.null.no                             html  
    hem.null.one                            html  
    hem.null.two                            html  
    hem.preproc                             html  
    mubcp                                   html  
    nonpar.error.Olig                       html  
    nonpar.no.error.Olig                    html  
    nonpar.rep.error.Olig                   html  
    par.error.Olig                          html  
    par.no.error.Olig                       html  
    par.rep.error.Olig                      html  
    pbrain                                  html  
    permut                                  html  
    quant.norm                              html  
    quant.normal                            html  
    quant.normal2                           html  
    quant.normalize                         html  
    remove.sig.genes                        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 'HEM' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hem.c -o hem.o
hem.c: In function 'onelayerhem':
hem.c:1390:12: warning: variable 'k' set but not used [-Wunused-but-set-variable]
  int i, j, k, m, n;
            ^
hem.c: In function 'chk_prt':
hem.c:1593:16: warning: variable 'l' set but not used [-Wunused-but-set-variable]
   int i, j, k, l;
                ^
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o HEM.dll tmp.def hem.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/HEM.buildbin-libdir/HEM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HEM' as HEM_1.62.0.zip
* DONE (HEM)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'HEM' successfully unpacked and MD5 sums checked

Tests output


Example timings

HEM.Rcheck/examples_i386/HEM-Ex.timings

nameusersystemelapsed
hem0.060.040.11
hem.eb.prior0.030.050.08
hem.fdr0.030.000.03
hem.preproc0.030.000.03

HEM.Rcheck/examples_x64/HEM-Ex.timings

nameusersystemelapsed
hem0.060.000.07
hem.eb.prior0.030.000.03
hem.fdr0.020.000.01
hem.preproc0.010.000.02