Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-02-22 11:37:06 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1552/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PING 2.46.0  (landing page)
Renan Sauteraud
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/PING
git_branch: RELEASE_3_18
git_last_commit: 49706e2
git_last_commit_date: 2023-10-24 09:49:31 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for PING on palomino4


To the developers/maintainers of the PING package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PING.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: PING
Version: 2.46.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PING.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings PING_2.46.0.tar.gz
StartedAt: 2024-02-22 05:01:01 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 05:06:12 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 311.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PING.Rcheck
Warnings: 4

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PING.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings PING_2.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/PING.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PING/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PING' version '2.46.0'
* 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 'PING' can be installed ... WARNING
Found the following significant warnings:
  ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'F:/biocbuild/bbs-3.18-bioc/meat/PING.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'PING' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'BSgenome' 'BiocGenerics' 'GenomicRanges' 'IRanges' 'S4Vectors' 'fda'
  'methods' 'stats' 'stats4'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot,ping-segReads: warning in symbols((map[, 1] + map[, 2])/2,
  rep(0.35, nMap), rectangle = cbind(map[, 2] - map[, 1], rep(0.6,
  nMap)), inches = FALSE, bg = grey(0.6), fg = 0, add = TRUE, xlim =
  c(m, M), ylim = c(0, 1)): partial argument match of 'rectangle' to
  'rectangles'
plot,ping-segReads : <anonymous>: warning in symbols(x@estimates$mu +
  shift * se(x), rep(0.5, K), rec = matrix(rep(c(147, 0.8), K), ncol =
  2, byrow = TRUE), inches = FALSE, bg = 0, fg = grey(abs(shift) *
  se(x)/(3 * (se(x)))), add = TRUE, xlim = c(m, M), ylim = c(0, 1), lwd
  = 2): partial argument match of 'rec' to 'rectangles'
plot,ping-segReads: warning in symbols(x@estimates$mu, rep(0.5, K), rec
  = matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches =
  FALSE, bg = "white", fg = grey(abs(0)), add = TRUE, xlim = c(m, M),
  ylim = c(0, 1)): partial argument match of 'rec' to 'rectangles'
CoverageTrack: no visible global function definition for 'resize'
CoverageTrack: no visible global function definition for 'seqnames'
CoverageTrack: no visible global function definition for 'start'
CoverageTrack: no visible global function definition for 'coverage'
CoverageTrack: no visible global function definition for 'width'
FilterPING: no visible global function definition for 'quantile'
NucleosomeTrack: no visible global function definition for 'as'
PostDelta: no visible global function definition for 'head'
PostDelta: no visible global function definition for 'as'
PostDup: no visible global function definition for 'head'
PostDup: no visible global function definition for 'as'
PostError: no visible global function definition for 'head'
PostError: no visible global function definition for 'summarySeg'
PostError: no visible global function definition for 'as'
PostSigma: no visible global function definition for 'head'
PostSigma: no visible global function definition for 'as'
RawReadsTrack: no visible global function definition for 'seqnames'
RawReadsTrack: no visible global function definition for 'start'
RawReadsTrack: no visible global function definition for 'end'
RawReadsTrack: no visible global function definition for 'strand'
make.thickthin: no visible global function definition for 'as.roman'
newPing: no visible global function definition for 'new'
newPingError: no visible global function definition for 'new'
newPingList: no visible global function definition for 'new'
postPING: no visible global function definition for 'as'
segmentPING: no visible global function definition for 'var'
segmentPING: no visible global function definition for 'seqlevels'
segmentPING: no visible global function definition for 'IRanges'
segmentPING: no visible global function definition for 'start'
segmentPING: no visible global function definition for 'end'
segmentPING: no visible global function definition for
  'candidate.region'
segmentPING: no visible global function definition for 'segChrRead'
segmentPING: no visible global function definition for 'segReadsListPE'
truncateResult: no visible global function definition for 'read.table'
as.data.frame,pingList: no visible global function definition for 'as'
plot,data.frame-data.frame: no visible global function definition for
  'pingFDR2'
plot,data.frame-data.frame: no visible global function definition for
  'tail'
plot,data.frame-data.frame: no visible global function definition for
  'head'
plot,ping-segReads : .densityMix: no visible global function definition
  for 'dt'
plot,ping-segReads: no visible global function definition for 'tail'
plot,pingError-segReads: no visible global function definition for
  'tail'
plot,pingList-pingList: no visible global function definition for
  'pingFDR'
show,pingList: no visible global function definition for 'getSlots'
summary,segReads: no visible global function definition for 'tail'
Undefined global functions or variables:
  IRanges as as.roman candidate.region coverage dt end getSlots head
  new pingFDR pingFDR2 quantile read.table resize segChrRead
  segReadsListPE seqlevels seqnames start strand summarySeg tail var
  width
Consider adding
  importFrom("methods", "as", "getSlots", "new")
  importFrom("stats", "dt", "end", "quantile", "start", "var")
  importFrom("utils", "as.roman", "head", "read.table", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'CoverageTrack' 'NucleosomeTrack' 'PING' 'RawReadsTrack'
  'makeGRangesOutput' 'newPing' 'newPingError' 'newPingList'
  'plotSummary' 'segmentPING'
Undocumented S4 classes:
  'ping' 'pingList' 'pingError'
Undocumented S4 methods:
  generic '[' and siglist 'pingList,ANY,ANY,ANY'
  generic 'as.data.frame' and siglist 'pingList'
  generic 'density' and siglist 'ping'
  generic 'density' and siglist 'pingError'
  generic 'density' and siglist 'pingList'
  generic 'plot' and siglist 'data.frame,data.frame'
  generic 'plot' and siglist 'ping,segReads'
  generic 'plot' and siglist 'pingError,segReads'
  generic 'plot' and siglist 'pingList,pingList'
  generic 'plot' and siglist 'pingList,segReadsList'
  generic 'show' and siglist 'pingList'
  generic 'summary' and siglist 'ping'
  generic 'summary' and siglist 'pingList'
  generic 'summary' and siglist 'segReads'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'postPING':
  'minK' 'maxK' 'tol' 'B' 'mSelect' 'mergePeaks' 'mapCorrect' 'xi'
  'rho' 'alpha' 'beta' 'lambda' 'dMu'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/PING/libs/x64/PING.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 files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'PING.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/PING.Rcheck/00check.log'
for details.



Installation output

PING.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL PING
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'PING' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  145 |   if( REAL(VECTOR_ELT(paraPrior, 5))[0]>0 & REAL(VECTOR_ELT(paraEM, 0))[0]==0) // automatically decide minK and maxKK for histone data, when minK=0
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
ping.c: In function 'ECM2':
ping.c:1536:16: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
 1536 |         double chiSum = 0, etaF, etaR, dd, cc;
      |                ^~~~~~
ping.c: In function 'mergePeak':
ping.c:3280:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
 3280 |   double tstat=0.0,tstatMax=0.0;
      |                    ^~~~~~~~
ping.c: In function 'fitModelK':
ping.c:477:25: warning: 'firstFit' may be used uninitialized [-Wmaybe-uninitialized]
  477 |         SEXP ans, temp, firstFit;
      |                         ^~~~~~~~
gcc -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-PING/00new/PING/libs/x64
** R
** 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 (PING)

Tests output


Example timings