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This page was generated on 2024-03-02 11:35:44 -0500 (Sat, 02 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 735/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowPeaks 1.48.0  (landing page)
Yongchao Ge
Snapshot Date: 2024-03-01 14:05:09 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/flowPeaks
git_branch: RELEASE_3_18
git_last_commit: d503362
git_last_commit_date: 2023-10-24 09:50:23 -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    OK    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 flowPeaks on nebbiolo2


To the developers/maintainers of the flowPeaks package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowPeaks.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: flowPeaks
Version: 1.48.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:flowPeaks.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings flowPeaks_1.48.0.tar.gz
StartedAt: 2024-03-01 22:16:52 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 22:17:18 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 26.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowPeaks.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:flowPeaks.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings flowPeaks_1.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/flowPeaks.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘flowPeaks/DESCRIPTION’ ... OK
* this is package ‘flowPeaks’ version ‘1.48.0’
* 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 ‘flowPeaks’ can be installed ... OK
* 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 ... 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 ... 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 ... NOTE
Call with DUP:
   .C("Rpack_kmeans", as.double(t(data.matrix(x))), as.integer(n), 
       as.integer(p), as.integer(K), cluster = integer(n), m = double(K * 
           p), nc = integer(K), S = double(K * p * p), Nb = integer(K * 
           K), twss = double(1), as.double(stime), DUP = FALSE, 
       PACKAGE = "flowPeaks")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
getS0K : <anonymous>: no visible global function definition for
  ‘nclass.FD’
getS0K: no visible global function definition for ‘median’
plot.flowPeaks: no visible global function definition for ‘hist’
plot.flowPeaks: no visible global function definition for ‘points’
plot.flowPeaks: no visible global function definition for ‘text’
plot.flowPeaks: no visible global function definition for ‘par’
plot.flowPeaks: no visible global function definition for ‘segments’
traditional.kmeans: no visible global function definition for ‘kmeans’
traditional.kmeans: no visible global function definition for ‘var’
Undefined global functions or variables:
  hist kmeans median nclass.FD par points segments text var
Consider adding
  importFrom("grDevices", "nclass.FD")
  importFrom("graphics", "hist", "par", "points", "segments", "text")
  importFrom("stats", "kmeans", "median", "var")
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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/flowPeaks/libs/flowPeaks.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘flowPeaks-guide.Rnw’... failed
 WARNING
Errors in running code in vignettes:
when running code in ‘flowPeaks-guide.Rnw’
  ...
Loading required package: flowCore
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘flowCore’

> samp <- read.FCS(system.file("extdata", "0877408774.B08", 
+     package = "flowCore"))

  When sourcing ‘flowPeaks-guide.R’:
Error: could not find function "read.FCS"
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘flowPeaks-guide.Rnw’ using Sweave

Starting the flow Peaks analysis...

    Task A: compute kmeans...

        ...finished summarization at 0.583 sec

    Task B: find peaks...
finished at 0.644 sec



Starting the flow Peaks analysis...

    Task A: compute kmeans...

        ...finished summarization at 0.348 sec

    Task B: find peaks...
finished at 0.393 sec


Loading required package: flowCore
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘flowCore’

Error: processing vignette 'flowPeaks-guide.Rnw' failed with diagnostics:
 chunk 17 (label = stage7) 
Error in read.FCS(system.file("extdata", "0877408774.B08", package = "flowCore")) : 
  could not find function "read.FCS"

--- failed re-building ‘flowPeaks-guide.Rnw’

SUMMARY: processing the following file failed:
  ‘flowPeaks-guide.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/flowPeaks.Rcheck/00check.log’
for details.



Installation output

flowPeaks.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL flowPeaks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘flowPeaks’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fpic  -g -O2  -Wall -c Rpack.cpp -o Rpack.o
Rpack.cpp: In function ‘void Rpack_relevel(int*, int*, int*, int*, int*, int*)’:
Rpack.cpp:141:25: warning: comparison of integer expressions of different signedness: ‘std::map<int, int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  141 |         if(levels.size()<(i+1)){
      |            ~~~~~~~~~~~~~^~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fpic  -g -O2  -Wall -c Rregistrate.cpp -o Rregistrate.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fpic  -g -O2  -Wall -c VoronoiDiagramGenerator.cpp -o VoronoiDiagramGenerator.o
VoronoiDiagramGenerator.cpp: In member function ‘void VoronoiDiagramGenerator::out_site(Site*)’:
VoronoiDiagramGenerator.cpp:803:12: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
  803 |         if(!triangulate & plot & !debug)
      |            ^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fpic  -g -O2  -Wall -c flowPeaks.cpp -o flowPeaks.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fpic  -g -O2  -Wall -c func_collect.cpp -o func_collect.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fpic  -g -O2  -Wall -c func_collect_supp.cpp -o func_collect_supp.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fpic  -g -O2  -Wall -c gvector_gmatrix.cpp -o gvector_gmatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fpic  -g -O2  -Wall -c kd_tree.cpp -o kd_tree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fpic  -g -O2  -Wall -c kmns.cpp -o kmns.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o flowPeaks.so Rpack.o Rregistrate.o VoronoiDiagramGenerator.o flowPeaks.o func_collect.o func_collect_supp.o gvector_gmatrix.o kd_tree.o kmns.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-flowPeaks/00new/flowPeaks/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 (flowPeaks)

Tests output


Example timings

flowPeaks.Rcheck/flowPeaks-Ex.timings

nameusersystemelapsed
flowPeaks1.9700.0482.019