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This page was generated on 2024-03-27 11:36:38 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 523/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.49.0  (landing page)
Moritz Gerstung
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/deepSNV
git_branch: devel
git_last_commit: 69c2512
git_last_commit_date: 2023-10-24 09:49:21 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for deepSNV on nebbiolo1


To the developers/maintainers of the deepSNV package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deepSNV.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: deepSNV
Version: 1.49.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings deepSNV_1.49.0.tar.gz
StartedAt: 2024-03-26 21:42:33 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 21:49:02 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 388.8 seconds
RetCode: 0
Status:   OK  
CheckDir: deepSNV.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings deepSNV_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/deepSNV.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 ‘deepSNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deepSNV’ version ‘1.49.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'parallel', 'IRanges', 'GenomicRanges', 'SummarizedExperiment',
  'Biostrings', 'VGAM', 'VariantAnnotation'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘deepSNV’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (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.
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 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
Packages in Depends field not imported from:
  ‘GenomicRanges’ ‘SummarizedExperiment’ ‘VariantAnnotation’ ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘estimateRho’ ‘logbb’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.deepSNVsingle: no visible global function definition for ‘pchisq’
.estimateDispersion: no visible global function definition for
  ‘optimize’
.makeVCFheader: no visible global function definition for ‘splitAsList’
.makeVCFheader: no visible global function definition for ‘DataFrame’
.significantSNV: no visible global function definition for ‘p.adjust’
.significantSNV: no visible global function definition for
  ‘scanVcfHeader’
.significantSNV: no visible global function definition for ‘VCF’
.significantSNV: no visible global function definition for ‘GRanges’
.significantSNV: no visible global function definition for ‘IRanges’
.significantSNV: no visible global function definition for ‘DataFrame’
.significantSNV: no visible global function definition for ‘SimpleList’
.significantSNV: no visible global function definition for ‘VCFHeader’
.significantSNV: no visible global function definition for ‘reference’
.significantSNV: no visible global function definition for ‘header’
bbb: no visible global function definition for ‘na.omit’
betabinLRT: no visible global function definition for ‘pchisq’
betabinLRT: no visible global function definition for ‘p.adjust’
bf2Vcf: no visible global function definition for ‘scanVcfHeader’
bf2Vcf: no visible global function definition for ‘VCF’
bf2Vcf: no visible global function definition for ‘GRanges’
bf2Vcf: no visible global function definition for ‘IRanges’
bf2Vcf: no visible global function definition for ‘DataFrame’
bf2Vcf: no visible global function definition for ‘VCFHeader’
bf2Vcf: no visible global function definition for ‘reference’
bf2Vcf: no visible global function definition for ‘header’
bf2Vcf: no visible global function definition for ‘SimpleList’
loadAllData: no visible global function definition for ‘mclapply’
makePrior: no visible global function definition for ‘info’
manhattanPlot: no visible global function definition for ‘legend’
mcChunk: no visible global function definition for ‘mclapply’
mutID: no visible global function definition for ‘seqnames’
p.combine: no visible global function definition for ‘pgamma’
plot.deepSNV: no visible global function definition for ‘legend’
plot.deepSNV: no visible global function definition for ‘par’
plot.deepSNV: no visible global function definition for ‘abline’
qvals2Vcf: no visible global function definition for ‘scanVcfHeader’
qvals2Vcf: no visible global function definition for ‘VCF’
qvals2Vcf: no visible global function definition for ‘GRanges’
qvals2Vcf: no visible global function definition for ‘IRanges’
qvals2Vcf: no visible global function definition for ‘DataFrame’
qvals2Vcf: no visible global function definition for ‘VCFHeader’
qvals2Vcf: no visible global function definition for ‘reference’
qvals2Vcf: no visible global function definition for ‘header’
qvals2Vcf: no visible global function definition for ‘SimpleList’
PCRTest,matrix-matrix: no visible global function definition for
  ‘pnorm’
estimateDirichlet,matrix: no visible binding for global variable
  ‘dirichlet’
estimateDirichlet,matrix: no visible global function definition for
  ‘coefficients’
normalize,matrix-matrix : <anonymous>: no visible global function
  definition for ‘loess’
overDispersion,matrix-matrix: no visible global function definition for
  ‘optimize’
overDispersion,matrix-matrix : <anonymous>: no visible global function
  definition for ‘na.omit’
Undefined global functions or variables:
  DataFrame GRanges IRanges SimpleList VCF VCFHeader abline
  coefficients dirichlet header info legend loess mclapply na.omit
  optimize p.adjust par pchisq pgamma pnorm reference scanVcfHeader
  seqnames splitAsList
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "coefficients", "loess", "na.omit", "optimize",
             "p.adjust", "pchisq", "pgamma", "pnorm")
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-3.19-bioc/R/site-library/deepSNV/libs/deepSNV.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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
RCC 5.862  0.104   5.967
* 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: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/deepSNV.Rcheck/00check.log’
for details.


Installation output

deepSNV.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘deepSNV’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c bam2R.cpp -o bam2R.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c betabinom.c -o betabinom.o
betabinom.c: In function ‘pbb’:
betabinom.c:27:16: warning: unused variable ‘log’ [-Wunused-variable]
   27 |         int i, log=0;
      |                ^~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o deepSNV.so bam2R.o betabinom.o /home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-deepSNV/00new/deepSNV/libs
** R
** data
** 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 (deepSNV)

Tests output


Example timings

deepSNV.Rcheck/deepSNV-Ex.timings

nameusersystemelapsed
Extract-methods0.0050.0040.009
RCC5.8620.1045.967
RF0.0000.0040.005
bam2R0.0240.0010.025
betabinLRT000
consensusSequence-methods0.0180.0000.018
control-methods0.0040.0000.004
coordinates-methods0.0030.0000.004
counts0.0200.0000.019
deepSNV-class1.3940.0271.423
deepSNV-methods0.3480.0040.352
deepSNV-package0.3030.0010.303
estimateDirichlet-methods2.4740.0762.550
estimateDispersion-methods2.7880.0162.804
makePrior0.0010.0000.000
manhattanPlot1.3060.0111.318
normalize-methods2.3280.0122.340
p.combine0.7580.0070.766
p.val-methods0.0000.0040.004
phiX2.6660.0112.678
pi0.4730.0040.477
plot.deepSNV0.1850.0080.193
repeatMask-methods0.8350.0480.883
shearwater0.5830.0360.619
show-deepSNV-method0.1700.0200.191
summary-methods0.2890.0200.309
test-methods0.0000.0040.005
trueSNVs0.0130.0040.017