| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:03 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1021/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| infercnv 1.18.1 (landing page) Christophe Georgescu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the infercnv package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/infercnv.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. |
| Package: infercnv |
| Version: 1.18.1 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:infercnv.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings infercnv_1.18.1.tar.gz |
| StartedAt: 2024-04-15 23:58:49 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-16 00:08:10 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 560.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: infercnv.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:infercnv.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings infercnv_1.18.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/infercnv.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 ‘infercnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘infercnv’ version ‘1.18.1’
* 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 ‘infercnv’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘HiddenMarkov:::makedensity’
See the note in ?`:::` about the use of this operator.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
inferCNVBayesNet 172.673 3.486 157.456
run 12.531 1.104 13.635
* 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 ...
‘inferCNV.Rmd’ using ‘UTF-8’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘inferCNV.Rmd’
...
> infercnv_obj = CreateInfercnvObject(raw_counts_matrix = "../inst/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz",
+ annotati .... [TRUNCATED]
INFO [2024-04-16 00:07:03] Parsing matrix: ../inst/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz
Warning in gzfile(raw_counts_matrix, "rt") :
cannot open compressed file '../inst/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz', probable reason 'No such file or directory'
When sourcing ‘inferCNV.R’:
Error: cannot open the connection
Execution halted
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/infercnv.Rcheck/00check.log’
for details.
infercnv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL infercnv ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘infercnv’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (infercnv)
infercnv.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
> #!/usr/bin/env Rscript
>
> library(testthat)
> library(infercnv)
>
> test_check("infercnv")
INFO [2024-04-16 00:06:51] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-04-16 00:06:51] subtracting mean(normal) per gene per cell across all data
INFO [2024-04-16 00:06:51] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-04-16 00:06:51] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-04-16 00:06:51] subtracting mean(normal) per gene per cell across all data
INFO [2024-04-16 00:06:51] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-04-16 00:06:51] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-04-16 00:06:51] subtracting mean(normal) per gene per cell across all data
INFO [2024-04-16 00:06:51] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-04-16 00:06:51] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-04-16 00:06:51] subtracting mean(normal) per gene per cell across all data
INFO [2024-04-16 00:06:51] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-04-16 00:06:51] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-04-16 00:06:51] subtracting mean(normal) per gene per cell across all data
INFO [2024-04-16 00:06:51] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-04-16 00:06:51] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-04-16 00:06:51] subtracting mean(normal) per gene per cell across all data
INFO [2024-04-16 00:06:51] -subtracting expr per gene, use_bounds=TRUE
WARN [2024-04-16 00:06:51] window length < 2, returning original unmodified data
WARN [2024-04-16 00:06:51] window length < 2, returning original unmodified data
INFO [2024-04-16 00:06:51] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2024-04-16 00:06:51] ::remove_outlier_norm: using hard thresholds: lower_bound: -1 upper_bound: 30
INFO [2024-04-16 00:06:51] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2024-04-16 00:06:51] ::remove_outlier_norm: using hard thresholds: lower_bound: 5 upper_bound: 15
INFO [2024-04-16 00:06:51] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2024-04-16 00:06:51] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2024-04-16 00:06:51] outlier bounds defined between: -0.5 - 17.75
INFO [2024-04-16 00:06:51] ::order_reduce:Start.
INFO [2024-04-16 00:06:51] ::order_reduce:Start.
INFO [2024-04-16 00:06:51] .order_reduce(): expr and order match.
INFO [2024-04-16 00:06:51] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2024-04-16 00:06:51] ::order_reduce:Start.
INFO [2024-04-16 00:06:51] .order_reduce(): expr and order match.
INFO [2024-04-16 00:06:51] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2024-04-16 00:06:51] ::order_reduce:Start.
INFO [2024-04-16 00:06:51] ::process_data:order_reduce:The position file and the expression file row (gene) names do not match.
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_infer_cnv.R:343:1', 'test_infer_cnv.R:349:1',
'test_infer_cnv.R:355:1'
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ]
>
> proc.time()
user system elapsed
12.133 0.705 12.828
infercnv.Rcheck/infercnv-Ex.timings
| name | user | system | elapsed | |
| CreateInfercnvObject | 0.090 | 0.012 | 0.102 | |
| apply_median_filtering | 4.485 | 0.268 | 4.753 | |
| color.palette | 0.002 | 0.000 | 0.002 | |
| filterHighPNormals | 0.012 | 0.000 | 0.012 | |
| inferCNVBayesNet | 172.673 | 3.486 | 157.456 | |
| plot_cnv | 0.689 | 0.088 | 0.713 | |
| plot_per_group | 1.198 | 0.076 | 1.274 | |
| plot_subclusters | 0.799 | 0.272 | 1.070 | |
| run | 12.531 | 1.104 | 13.635 | |
| sample_object | 0.025 | 0.000 | 0.025 | |