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This page was generated on 2021-10-13 15:05:28 -0400 (Wed, 13 Oct 2021).

CHECK results for MANOR on tokay2

To the developers/maintainers of the MANOR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MANOR.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 1027/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MANOR 1.64.0  (landing page)
Pierre Neuvial
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 2021)
git_url: https://git.bioconductor.org/packages/MANOR
git_branch: RELEASE_3_13
git_last_commit: 6c2e394
git_last_commit_date: 2021-05-19 11:36:36 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MANOR
Version: 1.64.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MANOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MANOR_1.64.0.tar.gz
StartedAt: 2021-10-13 00:53:00 -0400 (Wed, 13 Oct 2021)
EndedAt: 2021-10-13 00:54:19 -0400 (Wed, 13 Oct 2021)
EllapsedTime: 78.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MANOR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MANOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MANOR_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MANOR.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 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.64.0'
* 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 'MANOR' can be installed ... WARNING
Found the following significant warnings:
  nem_alg.c:801:7: warning: 'strncpy' output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MANOR.Rcheck/00install.out' for details.
* 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
* 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-3.13-bioc/R/library/MANOR/libs/i386/MANOR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/MANOR/libs/x64/MANOR.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
norm 5.36   0.06    5.43
** 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/MANOR.Rcheck/00check.log'
for details.



Installation output

MANOR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MANOR_1.64.0.tar.gz && rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MANOR.buildbin-libdir MANOR_1.64.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MANOR_1.64.0.zip && rm MANOR_1.64.0.tar.gz MANOR_1.64.0.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  446k  100  446k    0     0  1474k      0 --:--:-- --:--:-- --:--:-- 1477k

install for i386

* installing *source* package 'MANOR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rnem_arg.c -o Rnem_arg.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rnem_exe.c -o Rnem_exe.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exememo.c -o exememo.o
exememo.c: In function 'GenAlloc':
exememo.c:40:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                   ~~^
                                                   %d
      where, what, nelem, elsize);
                   ~~~~~                              
exememo.c:40:71: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                                     ~~^
                                                                     %d
      where, what, nelem, elsize);
                          ~~~~~~                                        
exememo.c:40:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                   ~~^
                                                   %d
      where, what, nelem, elsize);
                   ~~~~~                              
exememo.c:40:71: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                                     ~~^
                                                                     %d
      where, what, nelem, elsize);
                          ~~~~~~                                        
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",
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      where, what, nelem, elsize);
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_alg.c -o nem_alg.o
In function 'ClassifyByNemHeuBeta',
    inlined from 'ClassifyByNem' at nem_alg.c:578:13:
nem_alg.c:801:7: warning: 'strncpy' output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
       strncpy( namecri, NemParaP->OutBaseName, LEN_FILENAME ) ;
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_hlp.c -o nem_hlp.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_mod.c -o nem_mod.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_nei.c -o nem_nei.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_rnd.c -o nem_rnd.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_ver.c -o nem_ver.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c registerDynamicSymbols.c -o registerDynamicSymbols.o
C:/rtools40/mingw32/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 registerDynamicSymbols.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/MANOR.buildbin-libdir/00LOCK-MANOR/00new/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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/MANOR.buildbin-libdir/00LOCK-MANOR/00new/MANOR/help/manor.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 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 'MANOR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rnem_arg.c -o Rnem_arg.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rnem_exe.c -o Rnem_exe.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exememo.c -o exememo.o
exememo.c: In function 'GenAlloc':
exememo.c:40:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                   ~~^
                                                   %I64d
      where, what, nelem, elsize);
                   ~~~~~                              
exememo.c:40:71: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                                     ~~^
                                                                     %I64d
      where, what, nelem, elsize);
                          ~~~~~~                                        
exememo.c:40:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                   ~~^
                                                   %I64d
      where, what, nelem, elsize);
                   ~~~~~                              
exememo.c:40:71: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                                     ~~^
                                                                     %I64d
      where, what, nelem, elsize);
                          ~~~~~~                                        
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",
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      where, what, nelem, elsize);
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_alg.c -o nem_alg.o
In function 'ClassifyByNemHeuBeta',
    inlined from 'ClassifyByNem' at nem_alg.c:578:13:
nem_alg.c:801:7: warning: 'strncpy' output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
       strncpy( namecri, NemParaP->OutBaseName, LEN_FILENAME ) ;
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_hlp.c -o nem_hlp.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_mod.c -o nem_mod.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_nei.c -o nem_nei.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_rnd.c -o nem_rnd.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nem_ver.c -o nem_ver.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c registerDynamicSymbols.c -o registerDynamicSymbols.o
C:/rtools40/mingw64/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 registerDynamicSymbols.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/MANOR.buildbin-libdir/MANOR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MANOR' as MANOR_1.64.0.zip
* DONE (MANOR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MANOR' successfully unpacked and MD5 sums checked

Tests output


Example timings

MANOR.Rcheck/examples_i386/MANOR-Ex.timings

nameusersystemelapsed
arrayTrend0.450.030.49
detectSB0.400.010.42
flag.arrayCGH0.970.000.97
flag.summary0.110.020.13
flags0.110.020.12
genome.plot0.340.000.35
import0.160.000.15
nem2.630.002.62
norm5.360.065.43
qscore.arrayCGH0.120.000.12
qscore.summary0.440.010.45
qscores0.380.040.41
report.plot1.290.001.30
sort0.560.030.59
spatial0.350.060.41
to.flag0.390.030.42

MANOR.Rcheck/examples_x64/MANOR-Ex.timings

nameusersystemelapsed
arrayTrend0.390.020.40
detectSB0.360.010.38
flag.arrayCGH0.960.020.97
flag.summary0.090.000.09
flags0.080.000.08
genome.plot0.280.020.30
import0.130.000.12
nem2.340.002.34
norm4.470.014.49
qscore.arrayCGH0.090.000.09
qscore.summary0.360.000.36
qscores0.330.000.33
report.plot1.010.001.02
sort0.400.000.39
spatial0.400.020.42
to.flag0.530.000.53