Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:06 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for h5vc on nebbiolo2


To the developers/maintainers of the h5vc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/h5vc.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 887/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
h5vc 2.32.0  (landing page)
Paul Theodor Pyl
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/h5vc
git_branch: RELEASE_3_16
git_last_commit: c234c80
git_last_commit_date: 2022-11-01 11:08:58 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: h5vc
Version: 2.32.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:h5vc.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings h5vc_2.32.0.tar.gz
StartedAt: 2023-04-10 21:12:19 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:16:19 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 240.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: h5vc.Rcheck
Warnings: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:h5vc.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings h5vc_2.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/h5vc.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘h5vc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘h5vc’ version ‘2.32.0’
* 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 ‘h5vc’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’
See ‘/home/biocbuild/bbs-3.16-bioc/meat/h5vc.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘Rhtslib’ is only usable in R >= 3.0.2
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.h5dapplyIRanges: no visible binding for global variable ‘Sample’
binnedAFs : <anonymous>: no visible global function definition for
  ‘hist’
callVariantsPaired : <anonymous> : <anonymous>: no visible global
  function definition for ‘binom.test’
callVariantsPairedFisher : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for ‘fisher.test’
callVariantsPairedFisher : <anonymous> : <anonymous>: no visible
  binding for global variable ‘pValue’
callVariantsPairedFisher : <anonymous> : <anonymous>: no visible
  binding for global variable ‘BlockID’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable ‘Support’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable ‘AF’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable ‘SupFwd’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable ‘SupRev’
callVariantsSingle : <anonymous> : <anonymous> : binom.test.safe: no
  visible global function definition for ‘binom.test’
callVariantsSingle : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for ‘fisher.test’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable ‘BlockID’
mergeTallyFiles : <anonymous>: no visible binding for global variable
  ‘group’
mergeTallyFiles: no visible binding for global variable ‘SourceFile’
mismatchPlot: no visible binding for global variable ‘Sample’
plotMutationSpectrum: no visible binding for global variable
  ‘altAllele’
plotMutationSpectrum: no visible binding for global variable ‘tmp’
rerunBatchTallies: no visible binding for global variable ‘regID’
resizeCohort: no visible binding for global variable ‘newSamples’
tallyRangesBatch : <anonymous>: no visible binding for global variable
  ‘bamFiles’
tallyRangesBatch: no visible binding for global variable ‘verbose’
Undefined global functions or variables:
  AF BlockID Sample SourceFile SupFwd SupRev Support altAllele bamFiles
  binom.test fisher.test group hist newSamples pValue regID tmp verbose
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "binom.test", "fisher.test")
to your NAMESPACE file.
* 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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.16-bioc/R/site-library/h5vc/libs/h5vc.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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. 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
applyTallies       12.000  1.732  13.152
writeToTallyFile    6.101  1.770   7.134
callVariantsFisher  6.690  0.095   6.786
tallyRanges         5.153  1.412   5.869
* 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 ...
  ‘h5vc.simple.genome.browser.Rmd’... OK
  ‘h5vc.tour.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘h5vc.simple.genome.browser.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'h5vc.simple.genome.browser.knit'
--- finished re-building ‘h5vc.simple.genome.browser.Rmd’

--- re-building ‘h5vc.tour.Rmd’ using rmarkdown
Quitting from lines 234-254 (h5vc.tour.Rmd) 
Error: processing vignette 'h5vc.tour.Rmd' failed with diagnostics:
Timeout was reached: [www.ensembl.org:80] Operation timed out after 10000 milliseconds with 445685 bytes received
--- failed re-building ‘h5vc.tour.Rmd’

SUMMARY: processing the following file failed:
  ‘h5vc.tour.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/h5vc.Rcheck/00check.log’
for details.


Installation output

h5vc.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL h5vc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘h5vc’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function ‘int pileup_func_old(uint32_t, hts_pos_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:47:7: warning: unused variable ‘len’ [-Wunused-variable]
   47 |   int len = nttable->end - nttable->beg;
      |       ^~~
tallyBAM.cpp: In function ‘int pileup_func(uint32_t, hts_pos_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:96:7: warning: unused variable ‘len’ [-Wunused-variable]
   96 |   int len = nttable->end - nttable->beg;
      |       ^~~
tallyBAM.cpp: In function ‘int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)’:
tallyBAM.cpp:140:6: warning: unused variable ‘c’ [-Wunused-variable]
  140 |  int c = 0;
      |      ^
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: ‘int pileup_func_old(uint32_t, hts_pos_t, int, const bam_pileup1_t*, void*)’ defined but not used [-Wunused-function]
   43 | static int pileup_func_old(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data)
      |            ^~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o h5vc.so bam_plbuf.o tallyBAM.o /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-h5vc/00new/h5vc/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’
** testing if installed package keeps a record of temporary installation path
* DONE (h5vc)

Tests output

h5vc.Rcheck/tests/runTests.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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("h5vc")


RUNIT TEST PROTOCOL -- Mon Apr 10 21:15:46 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
h5vc RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' 
> 
> proc.time()
   user  system elapsed 
  5.700   0.239   5.926 

Example timings

h5vc.Rcheck/h5vc-Ex.timings

nameusersystemelapsed
applyTallies12.000 1.73213.152
batchTallies0.0010.0000.000
binGenome0.2390.0320.271
binnedAFs3.3160.3723.694
callVariants0.6240.0160.640
callVariantsFisher6.6900.0956.786
callVariantsSingle0.9150.0160.931
coverage2.7260.1032.836
geom_h5vc0.6120.0080.620
getSampleData0.0330.0250.087
h5dapply0.8380.0070.846
h5readBlock0.160.000.16
helpers0.1430.0000.143
mergeTallies0.6470.0240.671
mergeTallyFiles0.0010.0000.000
mismatchPlot4.1160.0914.208
mutationSpectrum3.6680.6044.273
plotMutationSpectrum2.7050.0512.756
prepareForHDF50.6990.0200.719
prepareTallyFile0.0640.0010.065
tallyBAM0.0400.0010.040
tallyRanges5.1531.4125.869
writeReference0.2130.0160.230
writeToTallyFile6.1011.7707.134