Kylie A. Bemis
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/matter |
| git_branch: RELEASE_3_14 |
| git_last_commit: 60a913c |
| git_last_commit_date: 2021-10-26 12:30:43 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:34 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the matter package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/matter.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1060/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| matter 1.20.0 (landing page) Kylie A. Bemis
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: matter |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings matter_1.20.0.tar.gz |
| StartedAt: 2022-04-12 08:04:38 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 08:05:54 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 76.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: matter.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings matter_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/matter.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.20.0’
* 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 ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
R 1.8Mb
libs 4.3Mb
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.14-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-3.14-bioc/R/bin/R CMD INSTALL matter
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘matter’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c altrep.cpp -o altrep.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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]
51 | 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:136:27: warning: ‘diff’ may be used uninitialized in this function [-Wmaybe-uninitialized]
136 | else if ( (mid == right && diff > 0) && (nearest || dright < tol) )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
In file included from init.cpp:5:
altrep.h:20:25: warning: ‘MatterAlt_string’ defined but not used [-Wunused-variable]
20 | static R_altrep_class_t MatterAlt_string;
| ^~~~~~~~~~~~~~~~
altrep.h:19:25: warning: ‘MatterAlt_real’ defined but not used [-Wunused-variable]
19 | static R_altrep_class_t MatterAlt_real;
| ^~~~~~~~~~~~~~
altrep.h:18:25: warning: ‘MatterAlt_integer’ defined but not used [-Wunused-variable]
18 | static R_altrep_class_t MatterAlt_integer;
| ^~~~~~~~~~~~~~~~~
altrep.h:17:25: warning: ‘MatterAlt_logical’ defined but not used [-Wunused-variable]
17 | static R_altrep_class_t MatterAlt_logical;
| ^~~~~~~~~~~~~~~~~
altrep.h:16:25: warning: ‘MatterAlt_raw’ defined but not used [-Wunused-variable]
16 | static R_altrep_class_t MatterAlt_raw;
| ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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:3409:25: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
3409 | 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]’:
matter.cpp:3409:25: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
3409 | 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 = unsigned char]’:
matter.cpp:3409:25: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
3409 | add<T,T>(x, y, i, atm, 0, count, skip);
| ^~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vectools.cpp -o vectools.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o matter.so altrep.o bsearch.o init.o matter.o utils.o vectools.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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: Matrix
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")
[ FAIL 0 | WARN 486 | SKIP 0 | PASS 343 ]
[ FAIL 0 | WARN 486 | SKIP 0 | PASS 343 ]
>
> proc.time()
user system elapsed
12.005 0.461 12.465
matter.Rcheck/matter-Ex.timings
| name | user | system | elapsed | |
| apply | 0.535 | 0.021 | 0.569 | |
| biglm | 0.027 | 0.000 | 0.028 | |
| binvec | 0.001 | 0.000 | 0.001 | |
| bsearch | 0.001 | 0.000 | 0.000 | |
| checksum | 0.008 | 0.000 | 0.008 | |
| chunk_apply | 0.134 | 0.004 | 0.139 | |
| colStats | 0.015 | 0.000 | 0.016 | |
| combine-method | 0.001 | 0.000 | 0.000 | |
| combiner-method | 0.01 | 0.00 | 0.01 | |
| delayed-ops | 0.006 | 0.000 | 0.007 | |
| drle-class | 0.000 | 0.000 | 0.001 | |
| keys-method | 0.006 | 0.000 | 0.007 | |
| lapply | 0.025 | 0.000 | 0.026 | |
| locmax | 0 | 0 | 0 | |
| matter-class | 0.020 | 0.000 | 0.021 | |
| matter_arr-class | 0.015 | 0.000 | 0.016 | |
| matter_df-class | 0.054 | 0.000 | 0.055 | |
| matter_fc-class | 0.018 | 0.000 | 0.019 | |
| matter_list-class | 0.012 | 0.000 | 0.012 | |
| matter_mat-class | 0.007 | 0.000 | 0.008 | |
| matter_str-class | 0.008 | 0.000 | 0.008 | |
| matter_vec-class | 0.003 | 0.000 | 0.004 | |
| prcomp | 0.022 | 0.000 | 0.022 | |
| profmem | 0.475 | 0.000 | 0.474 | |
| rep_vt | 0.002 | 0.000 | 0.002 | |
| scale | 0.008 | 0.000 | 0.008 | |
| sparse_mat-class | 0.005 | 0.000 | 0.005 | |
| stream-stats | 0.005 | 0.000 | 0.005 | |
| struct | 0.006 | 0.000 | 0.006 | |
| summary-stats | 0.008 | 0.000 | 0.009 | |
| tolerance-method | 0.005 | 0.000 | 0.004 | |
| uuid | 0.001 | 0.000 | 0.001 | |
| virtual_mat-class | 0.005 | 0.000 | 0.005 | |