| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:09 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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 | ||||
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To the developers/maintainers of the GPA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GPA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 857/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GPA 1.13.0 (landing page) Dongjun Chung
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: GPA |
| Version: 1.13.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data GPA |
| StartedAt: 2023-05-25 22:51:47 -0000 (Thu, 25 May 2023) |
| EndedAt: 2023-05-25 22:54:26 -0000 (Thu, 25 May 2023) |
| EllapsedTime: 159.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data GPA
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* checking for file ‘GPA/DESCRIPTION’ ... OK
* preparing ‘GPA’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GPA-example.Rnw’ using Sweave
Loading required package: Rcpp
Attaching package: ‘GPA’
The following object is masked from ‘package:stats’:
cov
Info: Number of GWAS data: 2
Info: Theoretically null distribution is used.
Info: No annotation data is provided.
Info: Lower bound for pi estimates is set to 1 / [number of SNPs].
Info: Number of GWAS data: 2
Info: Number of annotation data: 1
Info: Theoretically null distribution is used.
Info: Annotation data is provided.
Info: SNPs will be prioritized using annotation data.
Info: Lower bound for pi estimates is set to 1 / [number of SNPs].
Info: Association mapping based on the global FDR control at level 0.2.
Info: Association mapping based on the global FDR control at level 0.2.
Info: Number of GWAS data: 2
Info: Theoretically null distribution is used.
Info: No annotation data is provided.
Info: Fit the GPA model under H0 of the pleitropy test.
Info: Lower bound for pi estimates is set to 1 / [number of SNPs].
alpha: 0.595 0.544
( 0.007 0.004 )
GWAS combination: 00 10 01 11
pi: 0.803 0.047 0.092 0.059
( 0.003 0.003 0.003 0.003 )
q:
Annotation #1:
0.205 0.246 0.241 0.36
( 0.001 0.019 0.01 0.011 )
Ratio of q over baseline (00):
GWAS combination: 10 01 11
Annotation #1:
1.202 1.177 1.757
( 0.102 0.056 0.044 )
Error: processing vignette 'GPA-example.Rnw' failed with diagnostics:
unable to run pdflatex on 'GPA-example.tex'
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.15 ^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘GPA-example.Rnw’
SUMMARY: processing the following file failed:
‘GPA-example.Rnw’
Error: Vignette re-building failed.
Execution halted