Back to the "Multiple platform build/check report" A  B  C [D] E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for DESeq2 on zin1

This page was generated on 2016-09-21 03:38:13 -0700 (Wed, 21 Sep 2016).

Package 311/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DESeq2 1.13.14
Michael Love
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DESeq2
Last Changed Rev: 120796 / Revision: 121152
Last Changed Date: 2016-09-07 18:07:40 -0700 (Wed, 07 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DESeq2
Version: 1.13.14
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.13.14.tar.gz
StartedAt: 2016-09-20 05:29:48 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:33:38 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 230.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.13.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DESeq2.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESeq2’ version ‘1.13.14’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DESeq2’ 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
* 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 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘DESeq2.pdf’ from 785Kb to 660Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/DESeq2.Rcheck/00check.log’
for details.

DESeq2.Rcheck/00install.out:

* installing *source* package ‘DESeq2’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c DESeq2.cpp -o DESeq2.o
DESeq2.cpp: In function ‘double dlog_posterior(double, Rcpp::Matrix<14>::Row, Rcpp::Matrix<14>::Row, arma::mat, double, double, bool)’:
DESeq2.cpp:59:43: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::Mat<double>]’ is deprecated [-Wdeprecated-declarations]
   double ddetb = ( det(b) * trace(b.i(true) * db) );
                                           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:129:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: declared here
   arma_deprecated inline const Op<derived,op_inv> i(const bool ) const;   //!< kept only for compatibility with old user code
                                                   ^
DESeq2.cpp: In function ‘double d2log_posterior(double, Rcpp::Matrix<14>::Row, Rcpp::Matrix<14>::Row, arma::mat, double, double, bool)’:
DESeq2.cpp:87:27: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::Mat<double>]’ is deprecated [-Wdeprecated-declarations]
   arma::mat b_i = b.i(true);
                           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
 Base_inv_yes<derived>::i(const bool) const   // argument kept only for compatibility with old user code
 ^
DESeq2.cpp:90:43: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::Mat<double>]’ is deprecated [-Wdeprecated-declarations]
   double ddetb = ( det(b) * trace(b.i(true) * db) );
                                           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
 Base_inv_yes<derived>::i(const bool) const   // argument kept only for compatibility with old user code
 ^
DESeq2.cpp: In function ‘Rcpp::List fitBeta(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
DESeq2.cpp:348:62: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>]’ is deprecated [-Wdeprecated-declarations]
     hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i(true) * x.t() * sqrt(w);
                                                              ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
 Base_inv_yes<derived>::i(const bool) const   // argument kept only for compatibility with old user code
 ^
DESeq2.cpp:351:43: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>]’ is deprecated [-Wdeprecated-declarations]
     sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
                                           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
 Base_inv_yes<derived>::i(const bool) const   // argument kept only for compatibility with old user code
 ^
DESeq2.cpp:351:93: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>]’ is deprecated [-Wdeprecated-declarations]
     sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
                                                                                             ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
 Base_inv_yes<derived>::i(const bool) const   // argument kept only for compatibility with old user code
 ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/DESeq2.Rcheck/DESeq2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq2)

DESeq2.Rcheck/DESeq2-Ex.timings:

nameusersystemelapsed
DESeq1.1080.0081.114
DESeqDataSet0.0480.0000.047
coef2.1320.0042.138
collapseReplicates0.1240.0000.125
counts0.080.000.08
design0.0600.0000.059
dispersionFunction1.8440.0041.846
estimateDispersions0.6600.0000.661
estimateDispersionsGeneEst0.6760.0000.676
estimateSizeFactors0.1120.0000.112
estimateSizeFactorsForMatrix0.0680.0000.068
fpkm0.1480.0040.150
fpm0.1000.0120.113
makeExampleDESeqDataSet0.0600.0000.062
nbinomLRT1.3760.0001.379
nbinomWaldTest1.3960.0041.398
normalizationFactors1.5360.0001.537
plotCounts0.0840.0000.085
plotDispEsts0.6680.0080.676
plotMA1.4680.0041.475
plotPCA2.4000.0002.402
plotSparsity0.0760.0000.076
results4.4120.0124.423
rlog1.8720.0001.884
summary2.0360.0002.039
varianceStabilizingTransformation0.8680.0000.869
vst1.8200.0201.839