Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:09:48 -0400 (Wed, 16 Oct 2019).
Package 927/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
matter 1.10.0 Kylie A. Bemis
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: matter |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings matter_1.10.0.tar.gz |
StartedAt: 2019-10-16 02:54:22 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 02:55:44 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 81.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: matter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings matter_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/matter.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.10.0’ * 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-3.9-bioc/meat/matter.Rcheck/00check.log’ for details.
matter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL matter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘matter’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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*]’: 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]’: bsearch.cpp:133:26: warning: ‘diff’ may be used uninitialized in this function [-Wmaybe-uninitialized] else if ( mid == right && diff > 0 ) ~~~~~~~~~~~~~^~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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]’: matter.cpp:3538:33: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized] add(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]’: matter.cpp:3538:33: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized] add (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 = unsigned char]’: matter.cpp:3538:33: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized] add (x, y, i, atm, 0, count, skip); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ matter.cpp: In function ‘double var(MatterIterator &, bool) [with T = double]’: matter.cpp:4273:17: warning: ‘s_new’ may be used uninitialized in this function [-Wmaybe-uninitialized] s_new = s_old + (*x - m_old) * (*x - m_new); ^~~~~ matter.cpp:4272:37: warning: ‘m_new’ may be used uninitialized in this function [-Wmaybe-uninitialized] m_new = m_old + (*x - m_old) / n; ~~~~^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o matter.so bsearch.o init.o matter.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-matter/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (matter)
matter.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes" 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 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(matter) Loading required package: BiocParallel 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: 201 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 3.467 0.228 3.699
matter.Rcheck/matter-Ex.timings
name | user | system | elapsed | |
apply | 0.692 | 0.136 | 0.852 | |
biglm | 0.045 | 0.003 | 0.049 | |
bsearch | 0.001 | 0.000 | 0.001 | |
checksum | 0.012 | 0.003 | 0.016 | |
combiner-method | 0.018 | 0.000 | 0.017 | |
delayed-ops | 0.009 | 0.004 | 0.098 | |
drle-class | 0.001 | 0.001 | 0.001 | |
keys-method | 0.012 | 0.000 | 0.013 | |
lapply | 0.027 | 0.000 | 0.027 | |
matter-class | 0.019 | 0.000 | 0.019 | |
matter_arr-class | 0.012 | 0.000 | 0.012 | |
matter_df-class | 0.099 | 0.003 | 0.103 | |
matter_fc-class | 0.030 | 0.001 | 0.030 | |
matter_list-class | 0.023 | 0.000 | 0.024 | |
matter_mat-class | 0.007 | 0.004 | 0.011 | |
matter_str-class | 0.01 | 0.00 | 0.01 | |
matter_vec-class | 0.005 | 0.000 | 0.005 | |
prcomp | 0.038 | 0.003 | 0.042 | |
profmem | 0.488 | 0.000 | 0.488 | |
rep_vt | 0.003 | 0.000 | 0.003 | |
scale | 0.019 | 0.000 | 0.018 | |
sparse_mat-class | 0.011 | 0.000 | 0.011 | |
struct | 0.012 | 0.000 | 0.012 | |
summary-stats | 0.018 | 0.000 | 0.018 | |
tolerance-method | 0.008 | 0.000 | 0.009 | |
uuid | 0.002 | 0.000 | 0.001 | |
virtual_mat-class | 0.01 | 0.00 | 0.01 | |