| 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 |
This page was generated on 2016-10-13 12:43:44 -0700 (Thu, 13 Oct 2016).
| Package 295/1210 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| DESeq2 1.12.4 Michael Love
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] |  | |||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| Package: DESeq2 |
| Version: 1.12.4 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.12.4.tar.gz |
| StartedAt: 2016-10-13 01:14:21 -0700 (Thu, 13 Oct 2016) |
| EndedAt: 2016-10-13 01:18:32 -0700 (Thu, 13 Oct 2016) |
| EllapsedTime: 251.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DESeq2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.12.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.12.4’
* 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 685Kb to 573Kb
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-3.3-bioc/meat/DESeq2.Rcheck/00check.log’
for details.
DESeq2.Rcheck/00install.out:
* installing *source* package ‘DESeq2’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-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 (declared at /home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
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 (declared at /home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
arma::mat b_i = b.i(true);
^
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 (declared at /home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
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 (declared at /home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i(true) * x.t() * sqrt(w);
^
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 (declared at /home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
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 (declared at /home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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:
| name | user | system | elapsed | |
| DESeq | 1.143 | 0.000 | 1.156 | |
| DESeqDataSet | 0.042 | 0.000 | 0.042 | |
| coef | 2.113 | 0.004 | 2.119 | |
| collapseReplicates | 0.135 | 0.000 | 0.135 | |
| counts | 0.076 | 0.000 | 0.076 | |
| design | 0.060 | 0.000 | 0.061 | |
| dispersionFunction | 1.800 | 0.016 | 1.818 | |
| estimateDispersions | 0.723 | 0.004 | 0.727 | |
| estimateDispersionsGeneEst | 0.669 | 0.000 | 0.669 | |
| estimateSizeFactors | 0.121 | 0.000 | 0.121 | |
| estimateSizeFactorsForMatrix | 0.071 | 0.000 | 0.071 | |
| fpkm | 0.149 | 0.000 | 0.149 | |
| fpm | 0.107 | 0.008 | 0.115 | |
| makeExampleDESeqDataSet | 0.064 | 0.004 | 0.069 | |
| nbinomLRT | 1.083 | 0.004 | 1.096 | |
| nbinomWaldTest | 1.408 | 0.004 | 1.457 | |
| normalizationFactors | 1.432 | 0.004 | 1.472 | |
| plotCounts | 0.091 | 0.000 | 0.091 | |
| plotDispEsts | 0.730 | 0.004 | 0.736 | |
| plotMA | 1.468 | 0.004 | 1.474 | |
| plotPCA | 2.127 | 0.000 | 2.140 | |
| plotSparsity | 0.080 | 0.004 | 0.084 | |
| results | 4.478 | 0.008 | 4.557 | |
| rlog | 1.696 | 0.000 | 1.695 | |
| summary | 2.043 | 0.000 | 2.042 | |
| varianceStabilizingTransformation | 0.832 | 0.000 | 0.832 | |
| vst | 1.719 | 0.028 | 1.747 | |