| Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-04-18 11:32:20 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 2124/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TFBSTools 1.40.0 (landing page) Ge Tan
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | NA | ||||||||
|
To the developers/maintainers of the TFBSTools 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. |
| Package: TFBSTools |
| Version: 1.40.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TFBSTools_1.40.0.tar.gz |
| StartedAt: 2024-04-18 06:11:46 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 06:19:16 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 449.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TFBSTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TFBSTools_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/TFBSTools.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 ‘TFBSTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFBSTools’ version ‘1.40.0’
* 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 ‘TFBSTools’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 ... NOTE
Unexported objects imported by ':::' calls:
‘S4Vectors:::new_SimpleList_from_list’ ‘seqLogo:::pwm2ic’
See the note in ?`:::` about the use of this operator.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SiteSetList-class 42.809 2.034 45.653
searchAln-methods 9.778 0.114 10.013
toGRangesList-methods 7.804 0.061 8.039
SiteSet-class 5.673 0.285 6.043
* 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
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/TFBSTools.Rcheck/00check.log’
for details.
TFBSTools.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TFBSTools
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘TFBSTools’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
matrixAlignerDynamic.c:63:9: warning: variable 'sum_i' set but not used [-Wunused-but-set-variable]
float sum_i; // counter for sums in a position in profile1
^
matrixAlignerDynamic.c:64:9: warning: variable 'sum_j' set but not used [-Wunused-but-set-variable]
float sum_j; // counter for sums in a position in profile2
^
matrixAlignerDynamic.c:68:7: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
int counter; // another counter variable
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_TFBSTools.c -o R_init_TFBSTools.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.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-TFBSTools/00new/TFBSTools/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘seqLogo’ in package ‘TFBSTools’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘TFBSTools’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘TFBSTools’
** 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 (TFBSTools)
TFBSTools.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(TFBSTools)
>
> test_check("TFBSTools")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
18.568 0.832 19.814
TFBSTools.Rcheck/TFBSTools-Ex.timings
| name | user | system | elapsed | |
| IUPAC2Matrix | 0.001 | 0.000 | 0.002 | |
| MA0004.1 | 0.004 | 0.005 | 0.010 | |
| MotifSet-class | 0.000 | 0.000 | 0.001 | |
| PFMSimilarity-methods | 1.468 | 0.029 | 1.515 | |
| PWMSimilarity-methods | 0.007 | 0.003 | 0.011 | |
| SiteSet-class | 5.673 | 0.285 | 6.043 | |
| SiteSetList-class | 42.809 | 2.034 | 45.653 | |
| TFFM-class | 0.026 | 0.001 | 0.027 | |
| XMatrix-class | 0.016 | 0.002 | 0.017 | |
| XMatrixList-class | 0.003 | 0.003 | 0.006 | |
| deleteMatrixHavingID-methods | 0.064 | 0.045 | 0.112 | |
| dmmEM-methods | 0.000 | 0.001 | 0.000 | |
| getEmissionProb | 0.174 | 0.006 | 0.192 | |
| getMatrixByID-methods | 0.262 | 0.022 | 0.300 | |
| getMatrixSet-methods | 0.001 | 0.000 | 0.000 | |
| getPosProb | 0.169 | 0.003 | 0.179 | |
| makeFlatFileDir | 0 | 0 | 0 | |
| parseMEMEOutput | 0.160 | 0.002 | 0.164 | |
| permuteMatrix-methods | 0.066 | 0.003 | 0.070 | |
| rPWMDmm-methods | 0 | 0 | 0 | |
| readJASPARMatrix | 0.014 | 0.002 | 0.016 | |
| readXMLTFFM | 0.021 | 0.001 | 0.022 | |
| runMEME-methods | 0.000 | 0.001 | 0.000 | |
| sampleRanges | 0.269 | 0.009 | 0.280 | |
| searchAln-methods | 9.778 | 0.114 | 10.013 | |
| searchPairBSgenome-methods | 0 | 0 | 0 | |
| searchSeq-methods | 0.954 | 0.021 | 0.986 | |
| seqLogo | 0.766 | 0.157 | 0.932 | |
| shannon.entropy | 0 | 0 | 0 | |
| toGRangesList-methods | 7.804 | 0.061 | 8.039 | |
| toICM-methods | 0.012 | 0.003 | 0.016 | |
| toPWM-methods | 0.007 | 0.003 | 0.010 | |