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This page was generated on 2023-09-25 11:36:26 -0400 (Mon, 25 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1111/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MANOR 1.72.0  (landing page)
Pierre Neuvial
Snapshot Date: 2023-09-24 14:00:11 -0400 (Sun, 24 Sep 2023)
git_url: https://git.bioconductor.org/packages/MANOR
git_branch: RELEASE_3_17
git_last_commit: ac8c8fb
git_last_commit_date: 2023-04-25 09:42:45 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for MANOR on palomino3


To the developers/maintainers of the MANOR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MANOR
Version: 1.72.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MANOR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MANOR_1.72.0.tar.gz
StartedAt: 2023-09-25 03:53:24 -0400 (Mon, 25 Sep 2023)
EndedAt: 2023-09-25 03:54:07 -0400 (Mon, 25 Sep 2023)
EllapsedTime: 43.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MANOR.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MANOR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MANOR_1.72.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/MANOR.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.72.0'
* 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:
  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=]
  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=]
  nem_alg.c:801:7: warning: 'strncpy' output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
See 'F:/biocbuild/bbs-3.17-bioc/meat/MANOR.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 ... WARNING
checkRd: (7) detectSB.Rd:47: Invalid email address: Philippe.Hupe@.curie.fr
checkRd: (-1) flag.summary.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) flag.summary.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) genome.plot.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) report.plot.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) report.plot.Rd:29: Escaped LaTeX specials: \$
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.17-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 nor [v]sprintf. 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: 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/MANOR.Rcheck/00check.log'
for details.



Installation output

MANOR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MANOR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'MANOR' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rnem_arg.c -o Rnem_arg.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rnem_exe.c -o Rnem_exe.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -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=]
   40 |     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
      |                                                   ~~^
      |                                                     |
      |                                                     long int
      |                                                   %lld
   41 |             where, what, nelem, elsize);
      |                          ~~~~~                       
      |                          |
      |                          size_t {aka long long unsigned int}
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=]
   40 |     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
      |                                                                     ~~^
      |                                                                       |
      |                                                                       long int
      |                                                                     %lld
   41 |             where, what, nelem, elsize);
      |                                 ~~~~~~                                 
      |                                 |
      |                                 size_t {aka long long unsigned int}
exememo.c:40:5: warning: 'msg' may be used uninitialized [-Wmaybe-uninitialized]
   40 |     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   41 |             where, what, nelem, elsize);
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~
exememo.c:39:11: note: 'msg' was declared here
   39 |     char* msg;
      |           ^~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -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]
  801 |       strncpy( namecri, NemParaP->OutBaseName, LEN_FILENAME ) ;
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nem_hlp.c -o nem_hlp.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nem_mod.c -o nem_mod.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nem_nei.c -o nem_nei.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nem_rnd.c -o nem_rnd.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nem_ver.c -o nem_ver.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c registerDynamicSymbols.c -o registerDynamicSymbols.o
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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-MANOR/00new/MANOR/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (MANOR)

Tests output


Example timings

MANOR.Rcheck/MANOR-Ex.timings

nameusersystemelapsed
arrayTrend0.250.030.28
detectSB0.250.020.26
flag.arrayCGH0.790.080.86
flag.summary0.070.000.08
flags0.070.010.07
genome.plot0.310.020.33
import0.090.050.14
nem2.160.012.17
norm4.140.114.25
qscore.arrayCGH0.080.000.08
qscore.summary0.290.060.36
qscores0.360.020.50
report.plot1.020.001.02
sort0.300.000.29
spatial0.230.020.25
to.flag0.310.000.32