Robert Scharpf
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/VanillaICE |
| git_branch: RELEASE_3_17 |
| git_last_commit: c9915ed |
| git_last_commit_date: 2023-04-25 09:45:56 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:14 -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 2177/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VanillaICE 1.62.0 (landing page) Robert Scharpf
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the VanillaICE 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: VanillaICE |
| Version: 1.62.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VanillaICE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VanillaICE_1.62.0.tar.gz |
| StartedAt: 2023-10-19 09:14:37 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 09:22:49 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 491.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: VanillaICE.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VanillaICE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VanillaICE_1.62.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/VanillaICE.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 ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.62.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
'doMPI', 'doRedis'
* 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 ‘VanillaICE’ 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 startup messages can be suppressed ... NOTE
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘BSgenome.Hsapiens.UCSC.hg18’ ‘MatrixGenerics’
All declared Imports should be used.
* 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) VanillaICE.Rd:0-7: Must have a \description
* 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 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 include directives in Makefiles ... 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
ArrayViews-class 3.691 0.157 6.747
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/VanillaICE.Rcheck/00check.log’
for details.
VanillaICE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VanillaICE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘VanillaICE’ ... ** 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 rinit.c -o rinit.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 viterbi.c -o viterbi.o 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 VanillaICE.so rinit.o viterbi.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-VanillaICE/00new/VanillaICE/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ Creating a new generic function for ‘distance’ in package ‘VanillaICE’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ ** testing if installed package keeps a record of temporary installation path * DONE (VanillaICE)
VanillaICE.Rcheck/tests/doRUnit.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.
> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ pkg <- "VanillaICE"
+
+ if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+ path <- file.path( getwd(), "..", "inst", "unitTests" )
+ } else {
+ path <- system.file( package=pkg, "unitTests" )
+ }
+
+ cat( "\nRunning unit tests\n" )
+ print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ library( package=pkg, character.only=TRUE )
+
+ ##xmap.clear.cache()
+
+ ##Fail on warnings
+ options( warn=2 )
+
+ ## Get the pattern (if there is one?)
+ patt <- Sys.getenv( "RUNITFILEPATTERN" )
+ if( is.null( patt ) || nchar( patt ) == 0 ) {
+ testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ rngKind="Mersenne-Twister",
+ dirs=path,
+ testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ } else {
+ ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+ testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ rngKind="Mersenne-Twister",
+ testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+ dirs=path )
+ }
+ tests <- runTestSuite( testSuite )
+
+ pathReport <- file.path( path, "report" )
+
+ cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ printTextProtocol( tests, showDetails=FALSE )
+ printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ printTextProtocol( tests, showDetails=TRUE, fileName=paste( pathReport, ".txt", sep="" ) )
+
+ printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+
+ tmp <- getErrors( tests )
+ if( tmp$nFail > 0 | tmp$nErr > 0 ){
+ stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ", tmp$nErr, ")\n\n", sep=""))
+ }
+ } else {
+ warning( "cannot run unit tests -- package RUnit is not available" )
+ }
Running unit tests
$pkg
[1] "VanillaICE"
$getwd
[1] "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/VanillaICE.Rcheck/tests"
$pathToUnitTests
[1] "/private/tmp/RtmpJgMfI2/RLIBS_d1171088801e/VanillaICE/unitTests"
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: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to VanillaICE version 1.62.0
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:VanillaICE':
deletion
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:SummarizedExperiment':
shift
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
Loading required package: foreach
Loading required package: oligoClasses
Welcome to oligoClasses version 1.62.0
Executing test function test_ArrayViews ... done successfully.
Executing test function test_columnSubset ... Writing parsed files to /tmp/RtmpgC1mFj
done successfully.
Executing test function test_FilterParam ... done successfully.
Executing test function test_EmissionParam ... done successfully.
Executing test function test_SnpArrayExperiment ... Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'SnpDataFrame' for signature '"numeric"'
Error in VanillaICE:::SnpDataFrame(DataFrame(x = 3)) :
isSnp must be specified
Error in .local(object, isSnp, ...) : isSnp must be specified
Error in validObject(.Object) :
invalid class "RangedSummarizedExperiment" object:
'x@assays' is not parallel to 'x'
Error in SnpArrayExperiment(x, y, rowRanges = rowranges) :
isSnp must be the same length as rowRanges
done successfully.
Executing test function test_SnpArrayExperiment2 ... done successfully.
Executing test function test_SnpGRanges ... done successfully.
Executing test function test_acf2 ... done successfully.
Executing test function test_hmm_cnset ... Loading required package: crlmm
Loading required package: preprocessCore
Welcome to crlmm version 1.58.0
Attaching package: 'crlmm'
The following object is masked from 'package:VanillaICE':
genotypes
done successfully.
Executing test function test_state4 ... done successfully.
Executing test function test_rowMAD ... done successfully.
Executing test function test_scaleBy ... done successfully.
Executing test function test_duplicatedMapLocs ... done successfully.
Executing test function test_sweepMode.R ... done successfully.
Executing test function test_Viterbi ... done successfully.
Executing test function test_baf_emission ... done successfully.
Executing test function test_cn_NAs ... done successfully.
Executing test function test_emission_for_list ... done successfully.
Executing test function test_emission_update ... done successfully.
Executing test function test_multiple_chromosomes ... done successfully.
Executing test function test_null_assignment ... done successfully.
Executing test function test_oligoset_comparison ... done successfully.
Executing test function test_summarized_exp ... done successfully.
Executing test function test_updating ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Thu Oct 19 09:22:25 2023
***********************************************
Number of test functions: 24
Number of errors: 0
Number of failures: 0
1 Test Suite :
VanillaICE unit testing - 24 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
23.112 1.083 41.085
VanillaICE.Rcheck/VanillaICE-Ex.timings
| name | user | system | elapsed | |
| ArrayViews-class | 3.691 | 0.157 | 6.747 | |
| CopyNumScanParams | 0.002 | 0.001 | 0.003 | |
| EmissionParam-methods | 0.007 | 0.002 | 0.014 | |
| FilterParam-class | 0.002 | 0.001 | 0.003 | |
| HMM | 0.329 | 0.016 | 0.619 | |
| HMMList-class | 0.954 | 0.051 | 1.773 | |
| HmmParam | 0.004 | 0.001 | 0.008 | |
| IO | 0.010 | 0.001 | 0.017 | |
| IdiogramParams-class | 0.188 | 0.012 | 0.360 | |
| SnpArrayExperiment-class | 0.086 | 0.004 | 0.159 | |
| SnpExperiment | 0.136 | 0.005 | 0.250 | |
| SnpGRanges | 0.063 | 0.001 | 0.115 | |
| TransitionParam | 0.001 | 0.000 | 0.001 | |
| cnvFilter | 2.675 | 0.028 | 4.807 | |
| dropDuplicatedMapLocs | 0.134 | 0.003 | 0.243 | |
| emissionParam | 0.004 | 0.000 | 0.008 | |
| getExampleSnpExperiment | 0 | 0 | 0 | |
| getHmmParams | 0.010 | 0.001 | 0.019 | |
| hmm2 | 1.222 | 0.057 | 2.270 | |
| isHeterozygous | 0.302 | 0.028 | 0.568 | |
| parseSourceFile | 0.489 | 0.053 | 0.970 | |
| plotting | 0.908 | 0.042 | 1.649 | |
| robust-statistics | 0 | 0 | 0 | |
| snpArrayAssays | 0.014 | 0.001 | 0.030 | |
| sourcePaths | 0.010 | 0.000 | 0.017 | |
| sweepMode | 0.249 | 0.008 | 0.457 | |
| threshold | 0 | 0 | 0 | |
| viewports | 0.001 | 0.000 | 0.000 | |