DESeq2 1.12.4
Michael Love
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/DESeq2 | | Last Changed Rev: 119935 / Revision: 122332 | | Last Changed Date: 2016-08-07 07:08:50 -0700 (Sun, 07 Aug 2016) |
| 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 | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DESeq2_1.12.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/DESeq2.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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’ ... OK
* 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: OK
* installing *source* package ‘DESeq2’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c DESeq2.cpp -o DESeq2.o
DESeq2.cpp:59:37: warning: 'i' is deprecated [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
arma_deprecated inline const Op<derived,op_inv> i(const bool ) const; //!< kept only for compatibility with old user code
^
DESeq2.cpp:87:21: warning: 'i' is deprecated [-Wdeprecated-declarations]
arma::mat b_i = b.i(true);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
arma_deprecated inline const Op<derived,op_inv> i(const bool ) const; //!< kept only for compatibility with old user code
^
DESeq2.cpp:90:37: warning: 'i' is deprecated [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
arma_deprecated inline const Op<derived,op_inv> i(const bool ) const; //!< kept only for compatibility with old user code
^
DESeq2.cpp:348:56: warning: 'i' is deprecated [-Wdeprecated-declarations]
hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i(true) * x.t() * sqrt(w);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
arma_deprecated inline const Op<derived,op_inv> i(const bool ) const; //!< kept only for compatibility with old user code
^
DESeq2.cpp:351:37: warning: 'i' is deprecated [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
arma_deprecated inline const Op<derived,op_inv> i(const bool ) const; //!< kept only for compatibility with old user code
^
DESeq2.cpp:351:87: warning: 'i' is deprecated [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
arma_deprecated inline const Op<derived,op_inv> i(const bool ) const; //!< kept only for compatibility with old user code
^
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)