Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-01-17 12:23:56 -0500 (Wed, 17 Jan 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4330
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4289
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4413
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" 4341
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 281/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ccfindR 1.23.0  (landing page)
Jun Woo
Snapshot Date: 2024-01-16 14:00:13 -0500 (Tue, 16 Jan 2024)
git_url: https://git.bioconductor.org/packages/ccfindR
git_branch: devel
git_last_commit: aded0d3
git_last_commit_date: 2023-10-24 11:05:03 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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
merida1macOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for ccfindR on kunpeng2


To the developers/maintainers of the ccfindR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ccfindR.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ccfindR
Version: 1.23.0
Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings ccfindR_1.23.0.tar.gz
StartedAt: 2024-01-17 03:51:41 -0000 (Wed, 17 Jan 2024)
EndedAt: 2024-01-17 03:56:27 -0000 (Wed, 17 Jan 2024)
EllapsedTime: 286.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ccfindR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings ccfindR_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ccfindR.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ccfindR/DESCRIPTION’ ... OK
* this is package ‘ccfindR’ version ‘1.23.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ccfindR’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
* 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 ... NOTE
[kunpeng2:4045756] mca_base_component_repository_open: unable to open mca_pmix_ext3x: /usr/lib64/openmpi/lib/openmpi/mca_pmix_ext3x.so: undefined symbol: pmix_value_load (ignored)
[kunpeng2:4045756] [[12178,0],0] ORTE_ERROR_LOG: Not found in file ess_hnp_module.c at line 320
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  opal_pmix_base_select failed
  --> Returned value Not found (-13) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
[kunpeng2:4045529] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 716
[kunpeng2:4045529] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 172
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_ess_init failed
  --> Returned value Unable to start a daemon on the local node (-127) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems.  This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  ompi_mpi_init: ompi_rte_init failed
  --> Returned "Unable to start a daemon on the local node" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)
[kunpeng2:4045529] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
assignCelltype 16.899  1.792   18.74
factorize       8.350  0.019    8.39
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ccfindR.Rcheck/00check.log’
for details.



Installation output

ccfindR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL ccfindR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library’
* installing *source* package ‘ccfindR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c vbnmf_update.cpp -o vbnmf_update.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-devel/lib -L/usr/local/lib -o ccfindR.so RcppExports.o vbnmf_update.o -lgsl -lgslcblas -L/home/biocbuild/R/R-devel/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/00LOCK-ccfindR/00new/ccfindR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: ccfindR
*** 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 (ccfindR)

Tests output


Example timings

ccfindR.Rcheck/ccfindR-Ex.timings

nameusersystemelapsed
assignCelltype16.899 1.79218.740
basis-set-scNMFSet-method0.3090.0000.310
basis-set0.2400.0040.244
basis0.2770.0080.286
build_tree3.4690.0523.529
cell_map0.5800.0040.586
cluster_id3.4810.0003.489
coeff-set-scNMFSet-method0.2420.0080.250
coeff-set0.2490.0000.250
coeff0.2660.0000.267
colData-scNMFSet-method0.2870.0000.288
colData-set-scNMFSet-ANY-method0.2700.0040.275
counts-scNMFSet-method0.2270.0000.228
counts-set-scNMFSet-method0.2730.0000.273
factorize8.3500.0198.390
feature_map0.4530.0010.454
filter_cells0.2870.0000.288
filter_genes0.3440.0000.344
gene_map0.4460.0000.447
measure-set-scNMFSet-method0.2510.0000.251
measure-set0.2730.0000.273
measure0.2760.0000.276
meta_gene.cv4.2540.0004.264
meta_genes0.4390.0000.440
newick3.4640.0153.488
normalize_count0.2710.0040.275
optimal_rank4.1230.0004.132
plot_genes0.2270.0000.228
plot_tree3.5510.0083.568
ranks-set-scNMFSet-method0.2680.0000.269
ranks-set0.2650.0000.266
ranks0.2430.0080.252
read_10x0.6020.0000.604
remove_zeros0.2740.0000.276
rename_tips3.4610.0003.469
rowData-scNMFSet-method0.2170.0000.217
scNMFSet-class0.6870.0040.693
scNMFSet0.2030.0000.204
show-scNMFSet-method0.2030.0040.209
simulate_data0.1990.0000.200
simulate_whx3.4240.0003.432
vb_factorize3.4610.0003.469
visualize_clusters1.1790.0001.181
write_10x0.2270.0000.227
write_meta3.5020.0043.514