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CHECK report for MANOR on tokay1

This page was generated on 2019-04-13 11:19:48 -0400 (Sat, 13 Apr 2019).

Package 871/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MANOR 1.54.0
Pierre Neuvial
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/MANOR
Branch: RELEASE_3_8
Last Commit: 8031892
Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MANOR
Version: 1.54.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MANOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MANOR_1.54.0.tar.gz
StartedAt: 2019-04-13 03:29:51 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:31:43 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 112.0 seconds
RetCode: 0
Status:  OK  
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MANOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MANOR_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MANOR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.54.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'MANOR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'GLAD'
A package should be listed in only one of these fields.
* 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-3.8-bioc/R/library/MANOR/libs/i386/MANOR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/MANOR.Rcheck/00check.log'
for details.



Installation output

MANOR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MANOR_1.54.0.tar.gz && rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MANOR.buildbin-libdir MANOR_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MANOR_1.54.0.zip && rm MANOR_1.54.0.tar.gz MANOR_1.54.0.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  473k  100  473k    0     0  10.9M      0 --:--:-- --:--:-- --:--:-- 12.1M

install for i386

* installing *source* package 'MANOR' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Rnem_arg.c -o Rnem_arg.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Rnem_exe.c -o Rnem_exe.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c exememo.c -o exememo.o
exememo.c: In function 'GenAlloc':
exememo.c:41:6: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
      where, what, nelem, elsize);
      ^
exememo.c:41:6: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=]
exememo.c:40:5: warning: 'msg' may be used uninitialized in this function [-Wmaybe-uninitialized]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
     ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c nem_alg.c -o nem_alg.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c nem_hlp.c -o nem_hlp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c nem_mod.c -o nem_mod.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c nem_nei.c -o nem_nei.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c nem_rnd.c -o nem_rnd.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c nem_ver.c -o nem_ver.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o MANOR.dll tmp.def Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/MANOR.buildbin-libdir/MANOR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MANOR'
    finding HTML links ... done
    MANOR-internal                          html  
    arrayTrend                              html  
    detectSB                                html  
    flag.arrayCGH                           html  
    flag.summary                            html  
    flags                                   html  
    genome.plot                             html  
    html.report                             html  
    import                                  html  
    nem                                     html  
    norm                                    html  
    qscore                                  html  
    qscore.arrayCGH                         html  
    qscore.summary                          html  
    qscores                                 html  
    report.plot                             html  
    sort                                    html  
    spatial                                 html  
    to.flag                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MANOR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rnem_arg.c -o Rnem_arg.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rnem_exe.c -o Rnem_exe.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c exememo.c -o exememo.o
exememo.c: In function 'GenAlloc':
exememo.c:41:6: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
      where, what, nelem, elsize);
      ^
exememo.c:41:6: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=]
exememo.c:40:5: warning: 'msg' may be used uninitialized in this function [-Wmaybe-uninitialized]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nem_alg.c -o nem_alg.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nem_hlp.c -o nem_hlp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nem_mod.c -o nem_mod.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nem_nei.c -o nem_nei.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nem_rnd.c -o nem_rnd.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nem_ver.c -o nem_ver.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o MANOR.dll tmp.def Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/MANOR.buildbin-libdir/MANOR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MANOR' as MANOR_1.54.0.zip
* DONE (MANOR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MANOR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

MANOR.Rcheck/examples_i386/MANOR-Ex.timings

nameusersystemelapsed
arrayTrend0.340.030.38
detectSB0.380.020.39
flag.arrayCGH1.120.001.13
flag.summary0.110.010.12
flags0.110.020.13
genome.plot0.280.000.28
import0.190.020.20
nem3.420.003.43
norm1.060.031.09
qscore.arrayCGH0.130.000.12
qscore.summary0.610.010.63
qscores0.570.000.58
report.plot0.800.000.79
sort0.220.020.24
spatial0.360.010.37
to.flag0.390.000.39

MANOR.Rcheck/examples_x64/MANOR-Ex.timings

nameusersystemelapsed
arrayTrend0.50.00.5
detectSB0.50.00.5
flag.arrayCGH1.980.032.01
flag.summary0.170.010.19
flags0.160.020.17
genome.plot0.550.020.56
import0.260.000.27
nem3.380.013.39
norm1.050.021.07
qscore.arrayCGH0.090.000.09
qscore.summary0.710.030.74
qscores0.750.010.76
report.plot0.790.020.81
sort0.330.000.33
spatial0.300.030.33
to.flag0.340.000.34