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BioC 3.2: CHECK report for EDDA on windows1.bioconductor.org

This page was generated on 2015-10-27 17:31:04 -0400 (Tue, 27 Oct 2015).

Package 307/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EDDA 1.8.0
Chia Kuan Hui Burton , Niranjan Nagarajan
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/EDDA
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EDDA
Version: 1.8.0
Command: rm -rf EDDA.buildbin-libdir EDDA.Rcheck && mkdir EDDA.buildbin-libdir EDDA.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EDDA.buildbin-libdir EDDA_1.8.0.tar.gz >EDDA.Rcheck\00install.out 2>&1 && cp EDDA.Rcheck\00install.out EDDA-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=EDDA.buildbin-libdir --install="check:EDDA-install.out" --force-multiarch --no-vignettes --timings EDDA_1.8.0.tar.gz
StartedAt: 2015-10-27 01:28:43 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:32:38 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 234.7 seconds
RetCode: 0
Status:  OK  
CheckDir: EDDA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EDDA.buildbin-libdir EDDA.Rcheck && mkdir EDDA.buildbin-libdir EDDA.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EDDA.buildbin-libdir EDDA_1.8.0.tar.gz >EDDA.Rcheck\00install.out 2>&1 && cp EDDA.Rcheck\00install.out EDDA-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=EDDA.buildbin-libdir --install="check:EDDA-install.out" --force-multiarch --no-vignettes --timings EDDA_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/EDDA.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EDDA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EDDA' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Rcpp' 'parallel' 'ROCR' 'DESeq' 'baySeq' 'snow' 'edgeR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'EDDA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'parallel' 'methods' 'ROCR' 'DESeq' 'baySeq' 'snow' 'edgeR'
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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
exactTestMode: possible error in exactTestByDeviance(y1, y2, dispersion
  = dispersion, big.count = big.count): unused argument (big.count =
  big.count)
exactTestMode: possible error in exactTestBySmallP(y1, y2, dispersion =
  dispersion, big.count = big.count): unused argument (big.count =
  big.count)
generateData: no visible binding for global variable 'HBR'
generateData: no visible binding for global variable 'BP'
generateData: no visible binding for global variable 'Wu'
generateData: no visible binding for global variable 'SingleCell'
learn_parameter_DESeq: no visible global function definition for
  'fData'
learn_parameter_edgeR: no visible binding for global variable
  'mean_fc_relation'
run_Cuffdiff_Mode: no visible global function definition for
  'Cuffdiff_Mode'
* 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 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:/biocbld/bbs-3.2-bioc/meat/EDDA.buildbin-libdir/EDDA/libs/i386/EDDA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/biocbld/bbs-3.2-bioc/meat/EDDA.buildbin-libdir/EDDA/libs/x64/EDDA.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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [29s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
testDATs 16.56   0.08   16.94
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
testDATs 18.45   0.07   18.83
* 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: 5 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/EDDA.Rcheck/00check.log'
for details.


EDDA.Rcheck/00install.out:


install for i386

* installing *source* package 'EDDA' ...
** libs
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"C:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c cuffdiff.cpp -o cuffdiff.o
g++ -m32 -shared -s -static-libgcc -o EDDA.dll tmp.def cuffdiff.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/EDDA.buildbin-libdir/EDDA/libs/i386
** R
** data
** inst
** preparing package for lazy loading
No methods found in "baySeq" for requests: rbind
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "baySeq" for requests: rbind

install for x64

* installing *source* package 'EDDA' ...
** libs
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"C:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c cuffdiff.cpp -o cuffdiff.o
g++ -m64 -shared -s -static-libgcc -o EDDA.dll tmp.def cuffdiff.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/EDDA.buildbin-libdir/EDDA/libs/x64
** testing if installed package can be loaded
No methods found in "baySeq" for requests: rbind
* MD5 sums
packaged installation of 'EDDA' as EDDA_1.8.0.zip
* DONE (EDDA)

EDDA.Rcheck/examples_i386/EDDA-Ex.timings:

nameusersystemelapsed
EDDA-package1.250.001.25
computeAUC0.370.000.37
generateData3.910.164.08
plotPRC0.780.000.78
plotROC0.770.000.77
testDATs16.56 0.0816.94

EDDA.Rcheck/examples_x64/EDDA-Ex.timings:

nameusersystemelapsed
EDDA-package1.070.021.09
computeAUC0.330.000.33
generateData4.440.084.52
plotPRC1.140.011.15
plotROC1.110.001.11
testDATs18.45 0.0718.83