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This page was generated on 2024-03-28 11:36:14 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 221/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biovizBase 1.51.0  (landing page)
Michael Lawrence
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/biovizBase
git_branch: devel
git_last_commit: 226610a
git_last_commit_date: 2023-10-24 09:48:08 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for biovizBase on nebbiolo1


To the developers/maintainers of the biovizBase package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biovizBase.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

Package: biovizBase
Version: 1.51.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biovizBase.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biovizBase_1.51.0.tar.gz
StartedAt: 2024-03-27 20:42:31 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:48:32 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 361.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biovizBase.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biovizBase.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biovizBase_1.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biovizBase.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.51.0’
* 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: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/biovizBase.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether 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 ... NOTE
checkRd: (-1) pileupGRangesAsVariantTable.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pileupGRangesAsVariantTable.Rd:16-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pileupGRangesAsVariantTable.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pileupGRangesAsVariantTable.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pileupGRangesAsVariantTable.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
* 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 files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in GenenameFilter("BRCA1") : '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 14.374  0.765  15.161
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/biovizBase.Rcheck/00check.log’
for details.


Installation output

biovizBase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biovizBase
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘biovizBase’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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 /home/biocbuild/bbs-3.19-bioc/R/include/R_ext/RS.h:34,
                 from /home/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:38,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
/usr/include/string.h:159:33: note: expected ‘const char *’ but argument is of type ‘Rbyte *’ {aka ‘unsigned char *’}
  159 | extern int strncmp (const char *__s1, const char *__s2, size_t __n)
      |                     ~~~~~~~~~~~~^~~~
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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)

Tests output

biovizBase.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, 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 -- Wed Mar 27 20:48:10 2024 
*********************************************** 
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:
In GenenameFilter("ALDOA") : 'GenenameFilter' is deprecated.
Use 'GeneNameFilter' instead.
See help("Deprecated")
> 
> proc.time()
   user  system elapsed 
 18.487   1.084  19.586 

Example timings

biovizBase.Rcheck/biovizBase-Ex.timings

nameusersystemelapsed
CRC0.0000.0030.002
GCcontent0.4900.0290.518
addStepping-method0.5520.0920.644
aes-utils000
colorBlindSafePal0.0010.0000.000
containLetters0.0010.0000.000
crc1.GeRL0.0420.0110.054
crunch-method14.374 0.76515.161
darned_hg19_subset5000.0120.0040.016
flatGrl0.1870.0190.206
genesymbol0.0380.0000.038
getBioColor000
getFormalNames000
getGaps0.9910.0101.000
getIdeoGR0.1790.0080.187
getIdeogram000
hg19Ideogram0.0100.0010.011
hg19IdeogramCyto0.0120.0000.012
ideo0.0350.0040.039
ideoCyto0.0450.0000.045
isIdeogram0.0000.0030.004
isMatchedWithModel0.2900.0160.308
isSimpleIdeogram0.0220.0000.023
maxGap-method0.3030.0240.327
pileupAsGRanges000
pileupGRangesAsVariantTable000
plotColorLegend0.0000.0030.002
scale0.2090.0000.209
showColor000
shrinkageFun-method0.1660.0040.170
splitByFacets-method0.3540.0040.358
strip_formula_dots0.0010.0000.001
subsetArgsByFormals0.0010.0000.001
transform1.3690.2361.605
transformGRangesForEvenSpace0.1670.0100.176