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CHECK report for metaArray on tokay2

This page was generated on 2020-10-17 11:57:02 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE metaArray PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1029/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaArray 1.66.0
Hyungwon Choi
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/metaArray
Branch: RELEASE_3_11
Last Commit: 81724ce
Last Changed Date: 2020-04-27 14:12:41 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: metaArray
Version: 1.66.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings metaArray_1.66.0.tar.gz
StartedAt: 2020-10-17 05:48:17 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:49:43 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 86.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: metaArray.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings metaArray_1.66.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/metaArray.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 'metaArray/DESCRIPTION' ... OK
* this is package 'metaArray' version '1.66.0'
* 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 'metaArray' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'MergeMaid' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/metaArray.Rcheck/00install.out' for details.
* 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
poe.mcmc: no visible binding for global variable 'R0'
Undefined global functions or variables:
  R0
* checking Rd files ... NOTE
prepare_Rd: em.draw.Rd:28-30: Dropping empty section \examples
prepare_Rd: find.init.Rd:20-21: Dropping empty section \examples
prepare_Rd: fit.em.Rd:31-33: Dropping empty section \examples
prepare_Rd: poe.em.Rd:22: Dropping empty section \examples
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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-3.11-bioc/R/library/metaArray/libs/i386/metaArray.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/metaArray/libs/x64/metaArray.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (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: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/metaArray.Rcheck/00check.log'
for details.



Installation output

metaArray.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/metaArray_1.66.0.tar.gz && rm -rf metaArray.buildbin-libdir && mkdir metaArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaArray.buildbin-libdir metaArray_1.66.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL metaArray_1.66.0.zip && rm metaArray_1.66.0.tar.gz metaArray_1.66.0.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  661k  100  661k    0     0  2761k      0 --:--:-- --:--:-- --:--:-- 2838k

install for i386

* installing *source* package 'metaArray' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c contr.c -o contr.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dproc.c -o dproc.o
dproc.c: In function 'malloc_CH':
dproc.c:111:21: warning: variable 'num' set but not used [-Wunused-but-set-variable]
   int i, j, nr, nc, num;
                     ^~~
dproc.c: In function 'free_CH':
dproc.c:192:16: warning: unused variable 'nc' [-Wunused-variable]
   int num, nr, nc;
                ^~
dproc.c:192:12: warning: variable 'nr' set but not used [-Wunused-but-set-variable]
   int num, nr, nc;
            ^~
dproc.c:192:7: warning: variable 'num' set but not used [-Wunused-but-set-variable]
   int num, nr, nc;
       ^~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dproc2.c -o dproc2.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c intcor.c -o intcor.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lowess.c -o lowess.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mmath.c -o mmath.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c perm.c -o perm.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c poe.c -o poe.o
poe.c: In function 'poe_one_iter':
poe.c:131:53: warning: variable 'shift' set but not used [-Wunused-but-set-variable]
   double kappa_b, kappa_a, kappa_new, aaa, res_max, shift;
                                                     ^~~~~
poe.c:120:20: warning: variable 'accept' set but not used [-Wunused-but-set-variable]
   int nr,nc,tt,gg, accept;
                    ^~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o metaArray.dll tmp.def contr.o dproc.o dproc2.o intcor.o lowess.o mmath.o perm.o poe.o -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/metaArray.buildbin-libdir/00LOCK-metaArray/00new/metaArray/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
Warning: Package 'MergeMaid' is deprecated and will be removed from Bioconductor
  version 3.12
** help
*** installing help indices
  converting help for package 'metaArray'
    finding HTML links ... done
    Zscore                                  html  
    em.draw                                 html  
    find.init                               html  
    fit.em                                  html  
    intcor                                  html  
    logit                                   html  
    mdata                                   html  
    poe.em                                  html  
    poe.mcmc                                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 'metaArray' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c contr.c -o contr.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dproc.c -o dproc.o
dproc.c: In function 'malloc_CH':
dproc.c:111:21: warning: variable 'num' set but not used [-Wunused-but-set-variable]
   int i, j, nr, nc, num;
                     ^~~
dproc.c: In function 'free_CH':
dproc.c:192:16: warning: unused variable 'nc' [-Wunused-variable]
   int num, nr, nc;
                ^~
dproc.c:192:12: warning: variable 'nr' set but not used [-Wunused-but-set-variable]
   int num, nr, nc;
            ^~
dproc.c:192:7: warning: variable 'num' set but not used [-Wunused-but-set-variable]
   int num, nr, nc;
       ^~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dproc2.c -o dproc2.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c intcor.c -o intcor.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lowess.c -o lowess.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mmath.c -o mmath.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c perm.c -o perm.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c poe.c -o poe.o
poe.c: In function 'poe_one_iter':
poe.c:131:53: warning: variable 'shift' set but not used [-Wunused-but-set-variable]
   double kappa_b, kappa_a, kappa_new, aaa, res_max, shift;
                                                     ^~~~~
poe.c:120:20: warning: variable 'accept' set but not used [-Wunused-but-set-variable]
   int nr,nc,tt,gg, accept;
                    ^~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o metaArray.dll tmp.def contr.o dproc.o dproc2.o intcor.o lowess.o mmath.o perm.o poe.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/metaArray.buildbin-libdir/metaArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metaArray' as metaArray_1.66.0.zip
* DONE (metaArray)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'metaArray' successfully unpacked and MD5 sums checked

Tests output


Example timings

metaArray.Rcheck/examples_i386/metaArray-Ex.timings

nameusersystemelapsed
Zscore000
intcor000
poe.mcmc000

metaArray.Rcheck/examples_x64/metaArray-Ex.timings

nameusersystemelapsed
Zscore000
intcor000
poe.mcmc000