| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -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 219/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biovizBase 1.48.0 (landing page) Michael Lawrence
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK |  | |||||||
|
To the developers/maintainers of the biovizBase 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: biovizBase |
| Version: 1.48.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biovizBase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biovizBase_1.48.0.tar.gz |
| StartedAt: 2023-10-17 06:06:28 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 06:16:11 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 582.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biovizBase.Rcheck |
| Warnings: 2 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biovizBase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biovizBase_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biovizBase.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 ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.48.0’
* 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 ‘biovizBase’ can be installed ... WARNING
Found the following significant warnings:
bin_offsets.c:57:15: warning: passing 'Rbyte *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biovizBase.Rcheck/00install.out’ for details.
* 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 ... NOTE
Malformed Title field: should not end in a period.
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
'BSgenome' 'rtracklayer'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genSymbols: no visible binding for global variable 'start_location'
genSymbols: no visible binding for global variable 'end_location'
genSymbols: no visible binding for global variable 'Chromosome'
genSymbols: no visible binding for global variable 'symbol'
transformToLinkInCircle: no visible binding for global variable
'.circle.x'
transformToLinkInCircle: no visible binding for global variable
'.circle.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'from.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'from.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'to.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'to.y'
mold,ExpressionSet: no visible global function definition for 'exprs'
mold,ExpressionSet: no visible global function definition for 'pData'
mold,RleList: no visible binding for global variable 'xRleList'
mold,eSet: no visible global function definition for 'phenoData'
mold,eSet: no visible global function definition for 'melt'
mold,eSet: no visible global function definition for 'varLabels'
Undefined global functions or variables:
.circle.x .circle.y Chromosome end_location exprs from.x from.y melt
pData phenoData start_location symbol to.x to.y varLabels xRleList
* 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 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 ... WARNING
Found the following significant warnings:
Warning: 'GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
crunch-method 18.54 0.625 29.252
* 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: 2 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biovizBase.Rcheck/00check.log’
for details.
biovizBase.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biovizBase
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘biovizBase’ ...
** 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 R_init_biovizBase.c -o R_init_biovizBase.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bin_offsets.c -o bin_offsets.o
bin_offsets.c:57:15: warning: passing 'Rbyte *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/string.h:84:26: note: passing argument to parameter '__s1' here
int strncmp(const char *__s1, const char *__s2, size_t __n);
^
1 warning 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 biovizBase.so R_init_biovizBase.o bin_offsets.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-biovizBase/00new/biovizBase/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (biovizBase)
biovizBase.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("biovizBase")
Loading required package: ensembldb
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: GenomicRanges
Loading required package: stats4
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
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
The following object is masked from 'package:stats':
filter
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
RUNIT TEST PROTOCOL -- Tue Oct 17 06:15:54 2023
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
biovizBase RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning message:
'GenenameFilter' is deprecated.
Use 'GeneNameFilter' instead.
See help("Deprecated")
>
> proc.time()
user system elapsed
22.760 1.021 34.178
biovizBase.Rcheck/biovizBase-Ex.timings
| name | user | system | elapsed | |
| CRC | 0.002 | 0.002 | 0.007 | |
| GCcontent | 0.704 | 0.053 | 1.158 | |
| addStepping-method | 0.891 | 0.059 | 1.420 | |
| aes-utils | 0 | 0 | 0 | |
| colorBlindSafePal | 0 | 0 | 0 | |
| containLetters | 0.001 | 0.000 | 0.001 | |
| crc1.GeRL | 0.068 | 0.008 | 0.113 | |
| crunch-method | 18.540 | 0.625 | 29.252 | |
| darned_hg19_subset500 | 0.016 | 0.003 | 0.031 | |
| flatGrl | 0.314 | 0.012 | 0.496 | |
| genesymbol | 0.052 | 0.002 | 0.083 | |
| getBioColor | 0.000 | 0.000 | 0.001 | |
| getFormalNames | 0.000 | 0.001 | 0.000 | |
| getGaps | 1.434 | 0.024 | 2.263 | |
| getIdeoGR | 0.262 | 0.013 | 0.420 | |
| getIdeogram | 0 | 0 | 0 | |
| hg19Ideogram | 0.013 | 0.002 | 0.023 | |
| hg19IdeogramCyto | 0.015 | 0.002 | 0.026 | |
| ideo | 0.050 | 0.004 | 0.081 | |
| ideoCyto | 0.060 | 0.004 | 0.098 | |
| isIdeogram | 0.003 | 0.002 | 0.010 | |
| isMatchedWithModel | 0.545 | 0.037 | 0.897 | |
| isSimpleIdeogram | 0.029 | 0.002 | 0.048 | |
| maxGap-method | 0.473 | 0.016 | 0.747 | |
| pileupAsGRanges | 0.000 | 0.001 | 0.000 | |
| pileupGRangesAsVariantTable | 0 | 0 | 0 | |
| plotColorLegend | 0.002 | 0.001 | 0.004 | |
| scale | 0.339 | 0.012 | 0.536 | |
| showColor | 0.000 | 0.000 | 0.001 | |
| shrinkageFun-method | 0.275 | 0.012 | 0.438 | |
| splitByFacets-method | 0.548 | 0.020 | 0.834 | |
| strip_formula_dots | 0.001 | 0.000 | 0.002 | |
| subsetArgsByFormals | 0 | 0 | 0 | |
| transform | 1.969 | 0.214 | 3.346 | |
| transformGRangesForEvenSpace | 0.298 | 0.012 | 0.478 | |