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) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-01-17 12:23:56 -0500 (Wed, 17 Jan 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4330 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4289 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4413 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R 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 281/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ccfindR 1.23.0 (landing page) Jun Woo
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| 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 |
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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
###
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* 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.
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)
ccfindR.Rcheck/ccfindR-Ex.timings
| name | user | system | elapsed | |
| assignCelltype | 16.899 | 1.792 | 18.740 | |
| basis-set-scNMFSet-method | 0.309 | 0.000 | 0.310 | |
| basis-set | 0.240 | 0.004 | 0.244 | |
| basis | 0.277 | 0.008 | 0.286 | |
| build_tree | 3.469 | 0.052 | 3.529 | |
| cell_map | 0.580 | 0.004 | 0.586 | |
| cluster_id | 3.481 | 0.000 | 3.489 | |
| coeff-set-scNMFSet-method | 0.242 | 0.008 | 0.250 | |
| coeff-set | 0.249 | 0.000 | 0.250 | |
| coeff | 0.266 | 0.000 | 0.267 | |
| colData-scNMFSet-method | 0.287 | 0.000 | 0.288 | |
| colData-set-scNMFSet-ANY-method | 0.270 | 0.004 | 0.275 | |
| counts-scNMFSet-method | 0.227 | 0.000 | 0.228 | |
| counts-set-scNMFSet-method | 0.273 | 0.000 | 0.273 | |
| factorize | 8.350 | 0.019 | 8.390 | |
| feature_map | 0.453 | 0.001 | 0.454 | |
| filter_cells | 0.287 | 0.000 | 0.288 | |
| filter_genes | 0.344 | 0.000 | 0.344 | |
| gene_map | 0.446 | 0.000 | 0.447 | |
| measure-set-scNMFSet-method | 0.251 | 0.000 | 0.251 | |
| measure-set | 0.273 | 0.000 | 0.273 | |
| measure | 0.276 | 0.000 | 0.276 | |
| meta_gene.cv | 4.254 | 0.000 | 4.264 | |
| meta_genes | 0.439 | 0.000 | 0.440 | |
| newick | 3.464 | 0.015 | 3.488 | |
| normalize_count | 0.271 | 0.004 | 0.275 | |
| optimal_rank | 4.123 | 0.000 | 4.132 | |
| plot_genes | 0.227 | 0.000 | 0.228 | |
| plot_tree | 3.551 | 0.008 | 3.568 | |
| ranks-set-scNMFSet-method | 0.268 | 0.000 | 0.269 | |
| ranks-set | 0.265 | 0.000 | 0.266 | |
| ranks | 0.243 | 0.008 | 0.252 | |
| read_10x | 0.602 | 0.000 | 0.604 | |
| remove_zeros | 0.274 | 0.000 | 0.276 | |
| rename_tips | 3.461 | 0.000 | 3.469 | |
| rowData-scNMFSet-method | 0.217 | 0.000 | 0.217 | |
| scNMFSet-class | 0.687 | 0.004 | 0.693 | |
| scNMFSet | 0.203 | 0.000 | 0.204 | |
| show-scNMFSet-method | 0.203 | 0.004 | 0.209 | |
| simulate_data | 0.199 | 0.000 | 0.200 | |
| simulate_whx | 3.424 | 0.000 | 3.432 | |
| vb_factorize | 3.461 | 0.000 | 3.469 | |
| visualize_clusters | 1.179 | 0.000 | 1.181 | |
| write_10x | 0.227 | 0.000 | 0.227 | |
| write_meta | 3.502 | 0.004 | 3.514 | |