Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:08:01 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for matter on machv2


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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1060/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
matter 1.20.0  (landing page)
Kylie A. Bemis
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 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 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: matter
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:matter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings matter_1.20.0.tar.gz
StartedAt: 2022-01-20 14:40:13 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 14:42:29 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 135.4 seconds
RetCode: 0
Status:   OK  
CheckDir: matter.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:matter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings matter_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/matter.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ... 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 sizes of PDF files under ‘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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/matter.Rcheck/00check.log’
for details.



Installation output

matter.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL matter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘matter’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c altrep.cpp -o altrep.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bsearch.cpp -o bsearch.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matter.cpp -o matter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c vectools.cpp -o vectools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 matter.so altrep.o bsearch.o init.o matter.o utils.o vectools.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

matter.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0 | SKIP 0 | PASS 343 ]
> 
> proc.time()
   user  system elapsed 
 11.244   0.895  12.172 

Example timings

matter.Rcheck/matter-Ex.timings

nameusersystemelapsed
apply0.6540.0170.674
biglm0.0600.0070.067
binvec0.0020.0000.002
bsearch0.0010.0000.001
checksum0.0150.0020.017
chunk_apply0.2640.0180.281
colStats0.0340.0060.041
combine-method0.0020.0000.002
combiner-method0.0220.0020.024
delayed-ops0.0120.0030.015
drle-class0.0020.0010.001
keys-method0.0140.0020.015
lapply0.0560.0020.057
locmax0.0000.0000.001
matter-class0.0400.0040.045
matter_arr-class0.0260.0030.029
matter_df-class0.1040.0070.110
matter_fc-class0.0380.0020.040
matter_list-class0.0250.0040.028
matter_mat-class0.0150.0030.018
matter_str-class0.0180.0040.023
matter_vec-class0.0060.0020.007
prcomp0.0410.0070.048
profmem0.4450.0020.447
rep_vt0.0030.0010.005
scale0.0180.0020.020
sparse_mat-class0.0110.0030.012
stream-stats0.0090.0020.010
struct0.0130.0010.015
summary-stats0.0220.0030.025
tolerance-method0.0100.0010.010
uuid0.0010.0010.002
virtual_mat-class0.0090.0010.010