Multiple platform build/check report for BioC 3.21 - CHECK results for deepSNV on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
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 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: 1.53.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings deepSNV_1.53.0.tar.gz

StartedAt: 2024-12-23 21:16:27 -0500 (Mon, 23 Dec 2024)

EndedAt: 2024-12-23 21:22:36 -0500 (Mon, 23 Dec 2024)

EllapsedTime: 368.4 seconds

RetCode: 0

Status: OK

CheckDir: deepSNV.Rcheck

Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings deepSNV_1.53.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/deepSNV.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘deepSNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deepSNV’ version ‘1.53.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bf2Vcf.Rd: VCF, GRanges
  consensusSequence-methods.Rd: DNAString
  deepSNV-methods.Rd: GRanges
  qvals2Vcf.Rd: VCF, GRanges
  repeatMask-methods.Rd: DNAString
  summary-methods.Rd: VCF-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
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-3.21-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 5.786  0.126   5.912
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/deepSNV.Rcheck/00check.log’
for details.

Installation output

deepSNV.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL deepSNV
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘deepSNV’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c bam2R.cpp -o bam2R.o
bam2R.cpp:12: warning: "R_NO_REMAP" redefined
   12 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -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-3.21-bioc/R/lib -L/usr/local/lib -o deepSNV.so bam2R.o betabinom.o /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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

name	user	system	elapsed
Extract-methods	0.006	0.002	0.009
RCC	5.786	0.126	5.912
RF	0.003	0.002	0.005
bam2R	0.021	0.006	0.027
betabinLRT	0	0	0
consensusSequence-methods	0.018	0.003	0.021
control-methods	0.003	0.001	0.005
coordinates-methods	0.003	0.001	0.005
counts	0.020	0.001	0.021
deepSNV-class	1.405	0.025	1.431
deepSNV-methods	0.356	0.009	0.366
deepSNV-package	0.315	0.004	0.320
estimateDirichlet-methods	2.826	0.074	2.902
estimateDispersion-methods	2.784	0.041	2.825
makePrior	0	0	0
manhattanPlot	1.291	0.020	1.311
normalize-methods	2.193	0.021	2.214
p.combine	0.736	0.005	0.742
p.val-methods	0.003	0.001	0.003
phiX	2.535	0.016	2.551
pi	0.471	0.004	0.476
plot.deepSNV	0.182	0.006	0.188
repeatMask-methods	0.832	0.061	0.894
shearwater	0.578	0.078	0.657
show-deepSNV-method	0.169	0.011	0.179
summary-methods	0.280	0.019	0.299
test-methods	0.003	0.002	0.004
trueSNVs	0.008	0.002	0.009