| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:21 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the biovizBase package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 202/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biovizBase 1.47.0 (landing page) Michael Lawrence
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: biovizBase |
| Version: 1.47.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biovizBase.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings biovizBase_1.47.0.tar.gz |
| StartedAt: 2022-12-28 22:03:09 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 22:07:36 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 266.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biovizBase.Rcheck |
| Warnings: 2 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biovizBase.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings biovizBase_1.47.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/biovizBase.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biovizBase/DESCRIPTION' ... OK
* this is package 'biovizBase' version '1.47.0'
* 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 whether package 'biovizBase' can be installed ... WARNING
Found the following significant warnings:
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/biovizBase.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/biovizBase/libs/x64/biovizBase.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 11.56 0.55 12.31
* 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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/biovizBase.Rcheck/00check.log'
for details.
biovizBase.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL biovizBase
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'biovizBase' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
57 | if (strncmp(b, "BAI\1", 4))
| ^
| |
| Rbyte * {aka unsigned char *}
In file included from F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:34,
from F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:38,
from bin_offsets.h:1,
from bin_offsets.c:3:
c:\rtools43\x86_64-w64-mingw32.static.posix\include\string.h:86:35: note: expected 'const char *' but argument is of type 'Rbyte *' {aka 'unsigned char *'}
86 | int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
| ~~~~~~~~~~~~^~~~~
gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-biovizBase/00new/biovizBase/libs/x64
** 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
** 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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 -- Wed Dec 28 22:07:26 2022
***********************************************
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
14.54 1.32 15.92
biovizBase.Rcheck/biovizBase-Ex.timings
| name | user | system | elapsed | |
| CRC | 0 | 0 | 0 | |
| GCcontent | 0.38 | 0.03 | 0.44 | |
| addStepping-method | 1.41 | 0.05 | 1.45 | |
| aes-utils | 0 | 0 | 0 | |
| colorBlindSafePal | 0 | 0 | 0 | |
| containLetters | 0 | 0 | 0 | |
| crc1.GeRL | 0.05 | 0.00 | 0.05 | |
| crunch-method | 11.56 | 0.55 | 12.31 | |
| darned_hg19_subset500 | 0 | 0 | 0 | |
| flatGrl | 0.18 | 0.00 | 0.17 | |
| genesymbol | 0.03 | 0.00 | 0.03 | |
| getBioColor | 0 | 0 | 0 | |
| getFormalNames | 0 | 0 | 0 | |
| getGaps | 0.73 | 0.00 | 0.73 | |
| getIdeoGR | 0.13 | 0.03 | 0.16 | |
| getIdeogram | 0 | 0 | 0 | |
| hg19Ideogram | 0.01 | 0.00 | 0.01 | |
| hg19IdeogramCyto | 0.02 | 0.00 | 0.02 | |
| ideo | 0.01 | 0.02 | 0.03 | |
| ideoCyto | 0.04 | 0.02 | 0.05 | |
| isIdeogram | 0 | 0 | 0 | |
| isMatchedWithModel | 0.26 | 0.01 | 0.28 | |
| isSimpleIdeogram | 0.02 | 0.00 | 0.02 | |
| maxGap-method | 0.22 | 0.02 | 0.24 | |
| pileupAsGRanges | 0 | 0 | 0 | |
| pileupGRangesAsVariantTable | 0 | 0 | 0 | |
| plotColorLegend | 0 | 0 | 0 | |
| scale | 0.23 | 0.01 | 0.25 | |
| showColor | 0.02 | 0.00 | 0.00 | |
| shrinkageFun-method | 0.14 | 0.00 | 0.14 | |
| splitByFacets-method | 0.29 | 0.02 | 0.31 | |
| strip_formula_dots | 0 | 0 | 0 | |
| subsetArgsByFormals | 0 | 0 | 0 | |
| transform | 1.22 | 0.15 | 1.68 | |
| transformGRangesForEvenSpace | 0.14 | 0.02 | 0.16 | |