Back to Mac ARM64 build report for BioC 3.18
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-03-28 11:32:32 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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

Package 2045/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
srnadiff 1.22.2  (landing page)
Zytnicki Matthias
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/srnadiff
git_branch: RELEASE_3_18
git_last_commit: 7ddd95f
git_last_commit_date: 2024-03-07 15:02:50 -0400 (Thu, 07 Mar 2024)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for srnadiff on kjohnson1


To the developers/maintainers of the srnadiff package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: srnadiff
Version: 1.22.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings srnadiff_1.22.2.tar.gz
StartedAt: 2024-03-28 04:16:35 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 04:26:48 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 612.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: srnadiff.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings srnadiff_1.22.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/srnadiff.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘srnadiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘srnadiff’ version ‘1.22.2’
* package encoding: UTF-8
* 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 ‘srnadiff’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocManager’ ‘BiocStyle’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 ... NOTE
useEdgeR: no visible global function definition for 'model.matrix'
useEdgeR: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  model.matrix p.adjust
Consider adding
  importFrom("stats", "model.matrix", "p.adjust")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: parameters.Rd:38-40: Dropping empty section \details
checkRd: (5) plotRegions.Rd:115: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:116: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:117: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:118-119: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:120-121: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotRegions.Rd':
  ‘GdObject’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
plotRegions               13.308  1.515  14.286
countMatrix               11.998  1.115  12.301
parameters                10.339  2.252  10.654
srnadiff                   5.342  1.140   5.554
srnadiffDefaultParameters  5.204  1.120   5.356
regions                    5.198  1.012   5.360
* 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 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/srnadiff.Rcheck/00check.log’
for details.



Installation output

srnadiff.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘srnadiff’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_hmm.cpp -o rcpp_hmm.o
rcpp_hmm.cpp:109:17: warning: variable 'cpt' set but not used [-Wunused-but-set-variable]
            int cpt = 0;
                ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_ir.cpp -o rcpp_ir.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_main.cpp -o rcpp_main.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_utils.cpp -o rcpp_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c srnadiff_init.c -o srnadiff_init.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o srnadiff.so RcppExports.o rcpp_hmm.o rcpp_ir.o rcpp_main.o rcpp_utils.o srnadiff_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-srnadiff/00new/srnadiff/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (srnadiff)

Tests output

srnadiff.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(srnadiff)
> 
> test_check("srnadiff")
......[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
115.850  15.317 121.572 

Example timings

srnadiff.Rcheck/srnadiff-Ex.timings

nameusersystemelapsed
annotReg0.1610.0190.185
bamFiles0.2490.0220.274
chromosomeSizes0.0590.0050.064
countMatrix11.998 1.11512.301
coverages0.0930.0060.100
normFactors0.0570.0030.059
parameters10.339 2.25210.654
plotRegions13.308 1.51514.286
readAnnotation1.5410.0401.658
regions5.1981.0125.360
sampleInfo0.0600.0040.067
srnadiff5.3421.1405.554
srnadiffDefaultParameters5.2041.1205.356
srnadiffExample0.0590.0030.062
srnadiffExp1.5490.0701.673