matter 1.0.1
Kylie A. Bemis
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/matter | | Last Changed Rev: 127452 / Revision: 128728 | | Last Changed Date: 2017-03-15 22:03:50 -0400 (Wed, 15 Mar 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings matter_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/matter.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘matter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘matter’ version ‘1.0.1’
* 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 ‘matter’ 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 loading without being on the library search path ... 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 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 compiled code ... 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 ‘matter’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c matter.cpp -o matter.o
matter.cpp: In function ‘double var(MatterAccessor<double>&, bool)’:
matter.cpp:523:60: warning: ‘s_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
s_new = s_old + (*x - m_old) * (*x - m_new);
^
matter.cpp:522:37: warning: ‘m_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
m_new = m_old + (*x - m_old) / n;
^
In file included from matter.cpp:4:0:
matter.h: In member function ‘index_type Atoms::read_indices(RType*, dbl_index_type*, long int, std::size_t) [with RType = double; index_type = long int; dbl_index_type = double; std::size_t = long unsigned int]’:
matter.h:379:20: warning: ‘numRead’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return numRead;
^
matter.h: In member function ‘index_type Atoms::write_indices(RType*, dbl_index_type*, long int, std::size_t) [with RType = double; index_type = long int; dbl_index_type = double; std::size_t = long unsigned int]’:
matter.h:402:20: warning: ‘numWrote’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return numWrote;
^
matter.h: In member function ‘index_type Atoms::read_indices(RType*, dbl_index_type*, long int, std::size_t) [with RType = int; index_type = long int; dbl_index_type = double; std::size_t = long unsigned int]’:
matter.h:379:20: warning: ‘numRead’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return numRead;
^
matter.h: In member function ‘index_type Atoms::write_indices(RType*, dbl_index_type*, long int, std::size_t) [with RType = int; index_type = long int; dbl_index_type = double; std::size_t = long unsigned int]’:
matter.h:402:20: warning: ‘numWrote’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return numWrote;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o matter.so init.o matter.o utils.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/matter.Rcheck/matter/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘var’ in package ‘matter’
Creating a new generic function for ‘sd’ in package ‘matter’
Creating a new generic function for ‘apply’ in package ‘matter’
Creating a new generic function for ‘scale’ in package ‘matter’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (matter)