Back to Multiple platform build/check report for BioC 3.16
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-06-24 11:06:27 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 flowClust on palomino4


To the developers/maintainers of the flowClust package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowClust.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 670/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowClust 3.35.0  (landing page)
Greg Finak , Mike Jiang
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/flowClust
git_branch: master
git_last_commit: dab2912
git_last_commit_date: 2022-04-26 11:00:59 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flowClust
Version: 3.35.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowClust.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings flowClust_3.35.0.tar.gz
StartedAt: 2022-06-24 01:41:32 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 01:46:21 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 288.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowClust.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowClust.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings flowClust_3.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/flowClust.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'flowClust/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowClust' version '3.35.0'
* package encoding: UTF-8
* 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 'flowClust' can be installed ... OK
* 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 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
.flowClustK: no visible global function definition for 'var'
.flowClustK: no visible global function definition for 'qf'
.flowClustK: no visible global function definition for 'qchisq'
.flowClustK: no visible global function definition for 'quantile'
.flowClustK: no visible global function definition for 'kmeans'
.hist.flowClust: no visible global function definition for 'hist'
dmvt: no visible global function definition for 'mahalanobis'
hist.flowClust: no visible global function definition for 'hist'
hist.flowClust: no visible global function definition for 'curve'
hist.flowClust: no visible global function definition for 'stripchart'
hist.flowClustList: no visible global function definition for 'hist'
plot,flowClust-missing: no visible global function definition for
  'gray'
plot,flowClust-missing: no visible global function definition for
  'hist'
plot,flowClust-missing: no visible global function definition for
  'title'
plot,flowClust-missing: no visible global function definition for
  'points'
plot,flowClust-missing: no visible global function definition for 'qf'
plot,flowClust-missing: no visible global function definition for
  'qchisq'
plot,flowClustList-missing: no visible global function definition for
  'gray'
plot,flowDens-missing: no visible global function definition for
  'contour'
plot,flowDens-missing: no visible global function definition for
  'heat.colors'
plot,flowDens-missing: no visible global function definition for
  'rainbow'
plot,flowDens-missing: no visible global function definition for
  'terrain.colors'
plot,flowDens-missing: no visible global function definition for
  'topo.colors'
plot,flowDens-missing: no visible global function definition for
  'cm.colors'
plot,flowDens-missing: no visible global function definition for 'gray'
plot,flowDens-missing: no visible global function definition for
  'image'
plot,flowFrame-tmixFilterResult: no visible global function definition
  for 'hist'
ruleOutliers<-,flowClust-list: no visible global function definition
  for 'qf'
ruleOutliers<-,flowClust-list: no visible global function definition
  for 'qchisq'
Undefined global functions or variables:
  cm.colors contour curve gray heat.colors hist image kmeans
  mahalanobis points qchisq qf quantile rainbow stripchart
  terrain.colors title topo.colors var
Consider adding
  importFrom("grDevices", "cm.colors", "gray", "heat.colors", "rainbow",
             "terrain.colors", "topo.colors")
  importFrom("graphics", "contour", "curve", "hist", "image", "points",
             "stripchart", "title")
  importFrom("stats", "kmeans", "mahalanobis", "qchisq", "qf",
             "quantile", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'flowClust.Rd':
  'SimulateMixture'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 shell scripts ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/flowClust/libs/x64/flowClust.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. 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 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/flowClust.Rcheck/00check.log'
for details.



Installation output

flowClust.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/flowClust_3.35.0.tar.gz && rm -rf flowClust.buildbin-libdir && mkdir flowClust.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClust.buildbin-libdir flowClust_3.35.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL flowClust_3.35.0.zip && rm flowClust_3.35.0.tar.gz flowClust_3.35.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1589k  100 1589k    0     0  8330k      0 --:--:-- --:--:-- --:--:-- 8365k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'flowClust' ...
** using staged installation

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


** libs
rm -f BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o flowClust.dll
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c BoxCox.c -o BoxCox.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function 'BoxCoxGradientPriors':
BoxCoxPriors.c:57:16: warning: unused variable 'rowZ' [-Wunused-variable]
   57 |  rowPrecision, rowZ, rowLambda0;
      |                ^~~~
BoxCoxPriors.c:33:24: warning: unused variable 'kappa0' [-Wunused-variable]
   33 |  double *nu0 = p->nu0, kappa0 = p->kappa0;
      |                        ^~~~~~
BoxCoxPriors.c:32:7: warning: unused variable 'itersolve' [-Wunused-variable]
   32 |  int *itersolve = p->itersolve;
      |       ^~~~~~~~~
BoxCoxPriors.c:31:6: warning: unused variable 'iter' [-Wunused-variable]
   31 |  int iter = p->iter;
      |      ^~~~
BoxCoxPriors.c:28:6: warning: unused variable 'model' [-Wunused-variable]
   28 |  int model = *p->model;
      |      ^~~~~
BoxCoxPriors.c:23:14: warning: unused variable 'SumZlogY' [-Wunused-variable]
   23 |  gsl_vector *SumZlogY = p->SumZlogY;
      |              ^~~~~~~~
BoxCoxPriors.c:15:14: warning: unused variable 'Precision' [-Wunused-variable]
   15 |  gsl_matrix *Precision = p->Precision; // will be updated
      |              ^~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Nu.c -o Nu.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flowClust.c -o flowClust.o
flowClust.c: In function 'flowClust':
flowClust.c:48:2: warning: unused variable 'matrixZUY2' [-Wunused-variable]
   48 |  matrixZUY2;
      |  ^~~~~~~~~~
flowClust.c:46:48: warning: unused variable 'subRowZUY2' [-Wunused-variable]
   46 |  rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
      |                                                ^~~~~~~~~~
flowClust.c:46:39: warning: unused variable 'rowZUY2' [-Wunused-variable]
   46 |  rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
      |                                       ^~~~~~~
flowClust.c: In function 'ECMUpdateSigmaG2':
flowClust.c:1111:6: warning: unused variable 'i' [-Wunused-variable]
 1111 |  int i=0;
      |      ^
At top level:
flowClust.c:10:27: warning: 'CEntries' defined but not used [-Wunused-const-variable=]
   10 | static const R_CMethodDef CEntries[] = { { "flowClust", (DL_FUNC) & flowClust,
      |                           ^~~~~~~~
flowClust.c: In function 'flowClust':
flowClust.c:702:13: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
  702 |    status = gsl_min_fminimizer_set(s3, &F3, *nu, *nuLow, *nuUp);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:647:15: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
  647 |       nu_hi = gsl_root_fsolver_x_upper(s2);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:348:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
  348 |       x_hi = gsl_root_fsolver_x_upper(s);
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:207:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
  207 |       x_hi = gsl_root_fsolver_x_upper(s);
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ranMVNT.c -o ranMVNT.o
gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -lgsl -lgslcblas -lm -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/flowClust.buildbin-libdir/00LOCK-flowClust/00new/flowClust/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'Map' in package 'flowClust'
** 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
* MD5 sums
packaged installation of 'flowClust' as flowClust_3.35.0.zip
* DONE (flowClust)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'flowClust' successfully unpacked and MD5 sums checked

Tests output

flowClust.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(testthat)
> library(flowClust)

Attaching package: 'flowClust'

The following object is masked from 'package:graphics':

    box

The following object is masked from 'package:base':

    Map

> win32_flag = .Platform$OS.type == "windows" && .Machine$sizeof.pointer != 8
> if(!win32_flag)
+ test_check("flowClust")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 40 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Windows (1)
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 40 ]
> 
> #devtools::test("~/rglab/workspace/flowClust")
> 
> #taking quite some time , thus only for internal testing
> #test_file("~/rglab/workspace/flowClust/tests/testthat/flowClust-gated-data.R")
> #tools::checkDocFiles(dir = ".")
> 
> proc.time()
   user  system elapsed 
 210.43    0.70  211.15 

Example timings

flowClust.Rcheck/flowClust-Ex.timings

nameusersystemelapsed
box0.040.000.05
flowClust1.240.011.25
tmixFilter1.050.021.07