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"R CMD check" failure on Linux ARM64 #179
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Thanks for the report. Is there an EC2 image or similar that I could use to
investigate this?
…On Mon, Apr 3, 2023 at 4:36 AM Martin Grigorov ***@***.***> wrote:
Hello,
There is an initiative to support Linux ARM64 for Bioconductor. Probably
for 3.18.
R CMD check MAST_1.25.1.tar.gz fails with this output:
***@***.*** ~/git> R CMD build --keep-empty-dirs --no-resave-data MAST
* checking for file ‘MAST/DESCRIPTION’ ... OK
* preparing ‘MAST’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
WARNING: directory ‘MAST/docs/articles/MAITAnalysis_cache’ is empty
* building ‘MAST_1.25.1.tar.gz’
***@***.*** ~/git> R CMD check MAST_1.25.1.tar.gz
* using log directory ‘/home/biocbuild/git/MAST.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAST’ version ‘1.25.1’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MAST’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.2Mb
sub-directories of 1Mb or more:
data 3.7Mb
doc 5.2Mb
* 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 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[ FAIL 1 | WARN 26 | SKIP 5 | PASS 292 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-lrtest.R:25:5'): LRT and zlm are equivalent ──────────────────
all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 26 | SKIP 5 | PASS 292 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘MAITAnalysis.Rmd’ using ‘UTF-8’... OK
‘MAST-Intro.Rmd’ using ‘UTF-8’... OK
‘MAST-interoperability.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/git/MAST.Rcheck/00check.log’
for details.
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At AWS you could use Graviton 2/3 instances for Linux ARM64. Any compatible Linux image should be OK. |
Right on. How about a docker image or similar with Bioc devel for arm64?
…On Mon, Apr 3, 2023 at 7:16 AM Martin Grigorov ***@***.***> wrote:
At AWS you could use Graviton 2/3 instances for Linux ARM64. Any
compatible Linux image should be OK.
Otherwise please take a look at FrederickHuangLin/ANCOMBC#163 (comment)
<FrederickHuangLin/ANCOMBC#163 (comment)>
where another package maintainer recently asked me the same question.
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Right now only |
Hi,
But couldn't reproduce this failure with |
Hi @amcdavid ! Recently another Bioconductor developer went through the same and produced this Docker image - ghcr.io/grimbough/bioc-with-tinytex. |
Hello,
There is an initiative to support Linux ARM64 for Bioconductor. Probably for 3.18.
R CMD check MAST_1.25.1.tar.gz
fails with this output:The text was updated successfully, but these errors were encountered: