| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:03 -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 815/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicTuples 1.34.0 (landing page) Peter Hickey
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK |  | |||||||
|
To the developers/maintainers of the GenomicTuples 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: GenomicTuples |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicTuples.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicTuples_1.34.0.tar.gz |
| StartedAt: 2023-10-17 21:59:24 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 22:03:03 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 218.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicTuples.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicTuples.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicTuples_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenomicTuples.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 ‘GenomicTuples/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicTuples’ version ‘1.34.0’
* 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 ‘GenomicTuples’ 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 ... NOTE
Unexported objects imported by ':::' calls:
‘GenomicRanges:::extraColumnSlotNames’
‘GenomicRanges:::extraColumnSlots’
‘GenomicRanges:::extraColumnSlotsAsDF’ ‘S4Vectors:::VH_recycle’
‘S4Vectors:::orderBy’
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 ... WARNING
checkRd: (5) GTuples-class.Rd:127-155: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:181-189: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:190-205: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:206-211: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:212-218: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:227-230: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:232-234: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:236-240: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:242-246: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:248-258: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:260-263: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:265-269: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:271-280: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:282-286: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:288-292: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:294-302: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:304-309: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:311-316: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:318-323: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:325-330: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:332-335: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:346-352: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:354-360: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:362-367: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:369-377: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:385-389: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:391-396: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:398-406: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:408-417: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:426-431: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:433-436: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:438-443: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:445-465: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:467-471: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:473-478: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:480-490: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:491-504: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:506-520: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:527-541: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:120-134: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:135-141: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:142-149: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:150-155: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:156-161: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:162-166: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:167-171: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:172-179: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:180-184: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:185-190: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:65-69: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:78-81: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:82-85: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:86-89: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:90-94: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:95-101: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:102-107: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:108-119: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:120-129: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:130-136: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:137-141: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:142-146: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:147-155: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:156-162: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:163-168: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:169-174: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:175-180: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:181-184: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:196-202: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:204-210: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:212-218: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:220-228: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:236-242: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:243-245: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:248-254: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:262-268: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:269-273: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:274-278: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:279-285: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:286-298: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:299-304: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:305-311: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:319-325: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:326-331: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:332-335: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:343-347: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:348-355: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:356-360: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:361-367: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:368-373: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:374-386: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:387-393: \item in \describe must have non-empty label
* 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 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 ‘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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenomicTuples.Rcheck/00check.log’
for details.
GenomicTuples.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicTuples ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘GenomicTuples’ ... ** 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 -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 IPD.cpp -o IPD.o clang++ -arch arm64 -std=gnu++17 -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++17 -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 allTuplesSorted.cpp -o allTuplesSorted.o clang++ -arch arm64 -std=gnu++17 -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 pcompareGTuples.cpp -o pcompareGTuples.o 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 GenomicTuples.so IPD.o RcppExports.o allTuplesSorted.o pcompareGTuples.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-GenomicTuples/00new/GenomicTuples/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 (GenomicTuples)
GenomicTuples.Rcheck/tests/testthat.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.
> library(testthat)
> test_check("GenomicTuples")
Loading required package: GenomicTuples
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 1085 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 1085 ]
>
> proc.time()
user system elapsed
44.845 0.869 69.267
GenomicTuples.Rcheck/GenomicTuples-Ex.timings
| name | user | system | elapsed | |
| GTuples-class | 0.349 | 0.022 | 0.567 | |
| GTuples-comparison | 0.519 | 0.014 | 0.813 | |
| GTuplesList-class | 0.441 | 0.012 | 0.675 | |
| findOverlaps-methods | 0.537 | 0.012 | 0.846 | |
| illdefined-methods | 0.019 | 0.001 | 0.035 | |
| intra-tuple-methods | 0.132 | 0.004 | 0.218 | |
| nearest-methods | 0.678 | 0.009 | 1.040 | |
| tuples-squeezers | 0 | 0 | 0 | |