Sean Davis
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/ACME |
| git_branch: RELEASE_3_17 |
| git_last_commit: 083af12 |
| git_last_commit_date: 2023-04-25 09:45:10 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:57 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (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 13/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ACME 2.56.0 (landing page) Sean Davis
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the ACME 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: ACME |
| Version: 2.56.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ACME.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ACME_2.56.0.tar.gz |
| StartedAt: 2023-10-17 01:10:54 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 01:12:31 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 97.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ACME.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ACME.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ACME_2.56.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ACME.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 ‘ACME/DESCRIPTION’ ... OK
* this is package ‘ACME’ version ‘2.56.0’
* 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 ‘ACME’ 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 ... NOTE
installed size is 30.8Mb
sub-directories of 1Mb or more:
data 3.1Mb
extdata 27.3Mb
* 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 ... NOTE
.plotACMECalcSet: no visible global function definition for ‘par’
.plotACMECalcSet: no visible global function definition for ‘axis’
.plotACMECalcSet: no visible global function definition for ‘abline’
.plotACMESet: no visible global function definition for ‘par’
do.aGFF.calc: no visible global function definition for ‘quantile’
findClosestGene: no visible binding for global variable ‘refflat’
findClosestGene: no visible binding for '<<-' assignment to ‘refflat’
findRegions : <anonymous>: no visible global function definition for
‘median’
getRefflat: no visible global function definition for ‘download.file’
getRefflat: no visible global function definition for ‘read.delim’
plotgff: no visible global function definition for ‘par’
plotgffcalc: no visible global function definition for ‘par’
plotgffcalc: no visible global function definition for ‘axis’
plotgffcalc: no visible global function definition for ‘abline’
read.resultsGFF: no visible global function definition for ‘read.delim’
windowChisq: no visible global function definition for ‘pchisq’
write.bedGraph: no visible global function definition for ‘write.table’
write.sgr: no visible global function definition for ‘write.table’
plot,ACMECalcSet: no visible global function definition for ‘par’
plot,ACMECalcSet: no visible global function definition for ‘axis’
plot,ACMECalcSet: no visible global function definition for ‘abline’
plot,ACMESet: no visible global function definition for ‘par’
plot,aGFF: no visible global function definition for ‘par’
plot,aGFFCalc: no visible global function definition for ‘par’
plot,aGFFCalc: no visible global function definition for ‘axis’
plot,aGFFCalc: no visible global function definition for ‘abline’
Undefined global functions or variables:
abline axis download.file median par pchisq quantile read.delim
refflat write.table
Consider adding
importFrom("graphics", "abline", "axis", "par")
importFrom("stats", "median", "pchisq", "quantile")
importFrom("utils", "download.file", "read.delim", "write.table")
to your NAMESPACE file.
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
read.resultsGFF 3.592 0.096 5.635
getRefflat 1.883 0.085 5.671
findClosestGene 1.598 0.092 5.084
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ACME.Rcheck/00check.log’
for details.
ACME.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ACME
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘ACME’ ...
** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c windowChisq.c -o windowChisq.o
windowChisq.c:57:71: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
^
windowChisq.c:57:71: note: place parentheses around the '>' expression to silence this warning
while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
^
windowChisq.c:57:71: note: place parentheses around the & expression to evaluate it first
while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
^
(
windowChisq.c:62:70: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
^
windowChisq.c:62:70: note: place parentheses around the '<' expression to silence this warning
while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
^
windowChisq.c:62:70: note: place parentheses around the & expression to evaluate it first
while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
^
(
windowChisq.c:21:11: warning: unused variable 'xa' [-Wunused-variable]
double *xa,*xlocations,*xchivals;
^
windowChisq.c:86:20: warning: incompatible function pointer types initializing 'DL_FUNC' (aka 'void *(*)(void)') with an expression of type 'SEXP (*)(SEXP, SEXP, SEXP, SEXP, SEXP)' (aka 'struct SEXPREC *(*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)') [-Wincompatible-function-pointer-types]
{"windowChisq",&windowChisq,5},
^~~~~~~~~~~~
4 warnings generated.
clang -arch arm64 -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 ACME.so windowChisq.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-ACME/00new/ACME/libs
** R
** data
** 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 (ACME)
ACME.Rcheck/ACME-Ex.timings
| name | user | system | elapsed | |
| ACMECalcSet-class | 1.353 | 0.074 | 2.189 | |
| ACMESet-class | 0.473 | 0.016 | 0.763 | |
| aGFF-class | 0.512 | 0.020 | 0.807 | |
| aGFFCalc-class | 1.280 | 0.045 | 2.017 | |
| do.aGFF.calc | 1.320 | 0.041 | 2.063 | |
| example.agff | 0.473 | 0.015 | 0.748 | |
| findClosestGene | 1.598 | 0.092 | 5.084 | |
| findRegions | 2.321 | 0.067 | 3.605 | |
| generics | 0.450 | 0.015 | 0.708 | |
| getRefflat | 1.883 | 0.085 | 5.671 | |
| read.resultsGFF | 3.592 | 0.096 | 5.635 | |
| write.bedGraph | 1.688 | 0.150 | 2.847 | |
| write.sgr | 1.500 | 0.124 | 2.411 | |