Kylie A. Bemis
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/matter |
| Branch: RELEASE_3_8 |
| Last Commit: 4687b83 |
| Last Changed Date: 2018-12-18 16:44:00 -0400 (Tue, 18 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:24 -0400 (Tue, 16 Apr 2019).
| Package 888/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| matter 1.8.3 Kylie A. Bemis
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: matter |
| Version: 1.8.3 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings matter_1.8.3.tar.gz |
| StartedAt: 2019-04-16 01:09:15 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:10:27 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 72.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: matter.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings matter_1.8.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/matter.Rcheck’ * using R version 3.5.3 (2019-03-11) * 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 ‘1.8.3’ * 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 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 ... NOTE Note: information on .o files is not available * 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-3.8-bioc/meat/matter.Rcheck/00check.log’ for details.
matter.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL matter
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘matter’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bsearch.cpp -o bsearch.o
bsearch.cpp: In function ‘size_t binary_search(T, SEXP, size_t, size_t, double, int, int, bool) [with T = const char*; size_t = long unsigned int; SEXP = SEXPREC*]’:
bsearch.cpp:51:36: warning: ‘result’ may be used uninitialized in this function [-Wmaybe-uninitialized]
else if ( mid == right && result > 0 )
^
bsearch.cpp: In function ‘size_t binary_search(T, SEXP, size_t, size_t, double, int, int, bool) [with T = double; size_t = long unsigned int; SEXP = SEXPREC*]’:
bsearch.cpp:133:26: warning: ‘diff’ may be used uninitialized in this function [-Wmaybe-uninitialized]
else if ( mid == right && diff > 0 )
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c matter.cpp -o matter.o
matter.cpp: In member function ‘void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = double; index_t = long int; size_t = long unsigned int]’:
matter.cpp:3039:25: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
add<T,T>(x, y, i, atm, 0, count, skip);
^
matter.cpp: In member function ‘void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = int; index_t = long int; size_t = long unsigned int]’:
matter.cpp:3039:25: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
matter.cpp: In member function ‘void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = unsigned char; index_t = long int; size_t = long unsigned int]’:
matter.cpp:3039:25: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
matter.cpp: In function ‘double var(MatterIterator<T>&, bool) [with T = double]’:
matter.cpp:3713:17: warning: ‘s_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
s_new = s_old + (*x - m_old) * (*x - m_new);
^
matter.cpp:3712:17: warning: ‘m_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
m_new = m_old + (*x - m_old) / n;
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o matter.so bsearch.o init.o matter.o utils.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/matter/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘apply’ in package ‘matter’
Creating a new generic function for ‘scale’ in package ‘matter’
Creating a new generic function for ‘biglm’ in package ‘matter’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (matter)
matter.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(testthat)
> library(matter)
Loading required package: biglm
Loading required package: DBI
Attaching package: 'matter'
The following object is masked from 'package:biglm':
biglm
The following objects are masked from 'package:base':
apply, scale
>
> test_check("matter")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 175 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.124 0.144 4.307
matter.Rcheck/matter-Ex.timings
| name | user | system | elapsed | |
| apply | 0.072 | 0.000 | 0.080 | |
| biglm | 0.044 | 0.004 | 0.046 | |
| bsearch | 0 | 0 | 0 | |
| checksum | 0.012 | 0.004 | 0.016 | |
| combiner-method | 0.020 | 0.000 | 0.022 | |
| delayed-ops | 0.012 | 0.000 | 0.012 | |
| drle-class | 0.004 | 0.000 | 0.002 | |
| keys-method | 0.012 | 0.000 | 0.015 | |
| matter-class | 0.016 | 0.000 | 0.017 | |
| matter_arr-class | 0.008 | 0.004 | 0.010 | |
| matter_df-class | 0.032 | 0.000 | 0.035 | |
| matter_fc-class | 0.040 | 0.000 | 0.037 | |
| matter_list-class | 0.024 | 0.000 | 0.024 | |
| matter_mat-class | 0.012 | 0.000 | 0.011 | |
| matter_str-class | 0.016 | 0.000 | 0.017 | |
| matter_vec-class | 0.004 | 0.000 | 0.004 | |
| prcomp | 0.036 | 0.000 | 0.034 | |
| profmem | 0.436 | 0.000 | 0.441 | |
| rep_vt | 0.004 | 0.000 | 0.003 | |
| scale | 0.02 | 0.00 | 0.02 | |
| sparse_mat-class | 0.012 | 0.000 | 0.009 | |
| struct | 0.012 | 0.000 | 0.012 | |
| summary-stats | 0.012 | 0.000 | 0.015 | |
| tolerance-method | 0.012 | 0.000 | 0.009 | |
| uuid | 0.000 | 0.000 | 0.002 | |
| virtual_mat-class | 0.012 | 0.000 | 0.009 | |