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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 910/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Harman 1.28.0  (landing page)
Jason Ross
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Harman
git_branch: RELEASE_3_17
git_last_commit: 98d8921
git_last_commit_date: 2023-04-25 10:46:43 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Harman on kjohnson2


To the developers/maintainers of the Harman 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: Harman
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Harman.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Harman_1.28.0.tar.gz
StartedAt: 2023-10-18 00:16:49 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 00:18:53 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 124.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Harman.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Harman.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Harman_1.28.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Harman.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Harman/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Harman’ version ‘1.28.0’
* 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 ‘Harman’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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 ‘runTests.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-3.17-bioc-mac-arm64/meat/Harman.Rcheck/00check.log’
for details.



Installation output

Harman.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘Harman’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I.  -fPIC  -falign-functions=64 -Wall -g -O2  -c Harman.cpp -o Harman.o
In file included from Harman.cpp:182:
./CSelectRandom.h:283:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable]
                        size_t seed ;
                               ^
./CSelectRandom.h:372:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable]
                        size_t seed ;
                               ^
./CSelectRandom.h:394:35: warning: unused variable 'it1' [-Wunused-variable]
                        std::vector<double>::iterator  it1, it2 ;
                                                       ^
./CSelectRandom.h:394:40: warning: unused variable 'it2' [-Wunused-variable]
                        std::vector<double>::iterator  it1, it2 ;
                                                            ^
./CSelectRandom.h:392:11: warning: unused variable 'currindex' [-Wunused-variable]
                 size_t currindex ;
                        ^
./CSelectRandom.h:639:11: warning: unused variable 'time1' [-Wunused-variable]
                        double time1, time2 ;
                               ^
./CSelectRandom.h:638:25: warning: unused variable 'ts2' [-Wunused-variable]
                        struct timespec ts1, ts2 ;
                                             ^
./CSelectRandom.h:638:20: warning: unused variable 'ts1' [-Wunused-variable]
                        struct timespec ts1, ts2 ;
                                        ^
./CSelectRandom.h:639:18: warning: unused variable 'time2' [-Wunused-variable]
                        double time1, time2 ;
                                      ^
./CSelectRandom.h:1019:23: warning: unused variable 'randData2' [-Wunused-variable]
                                size_t randData1, randData2  ;
                                                  ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Harman.so Harman.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-Harman/00new/Harman/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 (Harman)

Tests output

Harman.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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.

> BiocGenerics:::testPackage("Harman")
First clustering, now find top two k, done. Reclustering, done.


RUNIT TEST PROTOCOL -- Wed Oct 18 00:18:36 2023 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Harman RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 
Warning message:
In kClusterMethylation(betas[1, , drop = FALSE], row_ks = ks[1]) :
  All rows have a cluster size of 1
> 
> proc.time()
   user  system elapsed 
 33.334   1.205  61.446 

Example timings

Harman.Rcheck/Harman-Ex.timings

nameusersystemelapsed
arrowPlot0.4650.0380.659
clusterStats0.0890.0222.333
discoverClusteredMethylation0.0800.0232.336
harman0.8140.0411.086
harmanresults0.5690.0300.754
kClusterMethylation0.0750.0182.268
pcaPlot0.4670.0260.621
plot.harmanresults0.4600.0250.628
prcompPlot0.2410.0150.324
reconstructData0.5240.0270.685
shiftBetas0.0010.0000.002
summary.harmanresults0.4650.0270.618