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CHECK report for aCGH on riesling1

This page was generated on 2020-10-28 13:27:25 -0400 (Wed, 28 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE aCGH PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 13/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aCGH 1.68.0
Peter Dimitrov
Snapshot Date: 2020-10-27 13:12:07 -0400 (Tue, 27 Oct 2020)
URL: https://git.bioconductor.org/packages/aCGH
Branch: RELEASE_3_12
Last Commit: 91f41a3
Last Changed Date: 2020-10-27 10:24:17 -0400 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK YES, new version is higher than 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 YES, new version is higher than in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: aCGH
Version: 1.68.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:aCGH.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings aCGH_1.68.0.tar.gz
StartedAt: 2020-10-27 20:01:06 -0400 (Tue, 27 Oct 2020)
EndedAt: 2020-10-27 20:02:42 -0400 (Tue, 27 Oct 2020)
EllapsedTime: 95.8 seconds
RetCode: 0
Status:  OK  
CheckDir: aCGH.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:aCGH.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings aCGH_1.68.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/aCGH.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 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.68.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'aCGH' can be installed ... OK
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  row.names.aCGH row.names<-.aCGH subset.hmm subset.hmm.merged
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* 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 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 'D:/biocbuild/bbs-3.12-bioc/R/library/aCGH/libs/i386/aCGH.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.12-bioc/R/library/aCGH/libs/x64/aCGH.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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
  'D:/biocbuild/bbs-3.12-bioc/meat/aCGH.Rcheck/00check.log'
for details.



Installation output

aCGH.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/aCGH_1.68.0.tar.gz && rm -rf aCGH.buildbin-libdir && mkdir aCGH.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=aCGH.buildbin-libdir aCGH_1.68.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL aCGH_1.68.0.zip && rm aCGH_1.68.0.tar.gz aCGH_1.68.0.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 1527k  100 1527k    0     0  5321k      0 --:--:-- --:--:-- --:--:-- 5321k

install for i386

* installing *source* package 'aCGH' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSEDOUBLE -g3    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c hmm.cpp -o hmm.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o aCGH.dll tmp.def hmm.o -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/aCGH.buildbin-libdir/00LOCK-aCGH/00new/aCGH/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'aCGH'
    finding HTML links ... done
    aCGH                                    html  
    aCGH.process                            html  
    aCGH.read.Sprocs                        html  
    aCGH.test                               html  
    clusterGenome                           html  
    colorectal                              html  
    computeSD.func                          html  
    fga.func                                html  
    find.genomic.events                     html  
    find.hmm.states                         html  
    findAber.func                           html  
    findAmplif.func                         html  
    findOutliers.func                       html  
    findTrans.func                          html  
    gainLoss                                html  
    heatmap                                 html  
    human.chrom.info.Jul03                  html  
    human.chrom.info.May04                  html  
    impute.HMM                              html  
    impute.lowess                           html  
    mergeFunc                               html  
    mergeLevels                             html  
    plotFreqStat                            html  
    plotGenome                              html  
    plotHmmStates                           html  
    plotSummaryProfile                      html  
    states.hmm.func                         html  
    summarize.clones                        html  
    threshold.func                          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 'aCGH' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSEDOUBLE -g3    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c hmm.cpp -o hmm.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o aCGH.dll tmp.def hmm.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/aCGH.buildbin-libdir/aCGH/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'aCGH' as aCGH_1.68.0.zip
* DONE (aCGH)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'aCGH' successfully unpacked and MD5 sums checked

Tests output


Example timings

aCGH.Rcheck/examples_i386/aCGH-Ex.timings

nameusersystemelapsed
aCGH0.980.111.47
aCGH.process0.020.000.01
aCGH.read.Sprocs0.070.030.09
clusterGenome0.970.041.28
colorectal0.150.100.31
fga.func0.360.030.39
find.hmm.states0.270.000.26
gainLoss0.590.050.69
heatmap0.340.040.43
impute.HMM0.630.050.67
impute.lowess0.050.000.05
mergeLevels0.070.020.09
plotFreqStat2.190.022.20
plotGenome1.220.111.50
plotHmmStates0.200.040.39
plotSummaryProfile0.800.050.87
summarize.clones0.160.050.20
threshold.func0.170.010.19

aCGH.Rcheck/examples_x64/aCGH-Ex.timings

nameusersystemelapsed
aCGH0.910.091.33
aCGH.process0.030.000.03
aCGH.read.Sprocs0.090.000.09
clusterGenome0.990.051.26
colorectal0.340.030.41
fga.func0.130.020.14
find.hmm.states0.180.010.20
gainLoss0.440.000.44
heatmap0.350.020.37
impute.HMM0.540.030.58
impute.lowess0.030.010.04
mergeLevels0.070.000.08
plotFreqStat2.180.022.20
plotGenome0.970.111.23
plotHmmStates0.210.040.33
plotSummaryProfile0.400.050.53
summarize.clones0.280.030.31
threshold.func0.130.000.13