| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 928/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GWASTools 1.52.0 (landing page) Stephanie M. Gogarten
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the GWASTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GWASTools.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: GWASTools |
| Version: 1.52.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GWASTools |
| StartedAt: 2025-01-08 21:59:52 -0000 (Wed, 08 Jan 2025) |
| EndedAt: 2025-01-08 22:00:46 -0000 (Wed, 08 Jan 2025) |
| EllapsedTime: 54.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GWASTools
###
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* checking for file ‘GWASTools/DESCRIPTION’ ... OK
* preparing ‘GWASTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Affymetrix.Rmd’ using rmarkdown
Error: processing vignette 'Affymetrix.Rmd' failed with diagnostics:
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- failed re-building ‘Affymetrix.Rmd’
--- re-building ‘DataCleaning.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
adding variables: genotype
adding variables: quality, X, Y
adding variables: BAlleleFreq, LogRRatio
Wed Jan 8 22:00:29 2025 Load genotype dataset ...
Wed Jan 8 22:00:30 2025 1/3 A
Wed Jan 8 22:00:30 2025 2/3 B
Wed Jan 8 22:00:30 2025 3/3 C
Loading required package: gdsfmt
All row numbers refer to row in the full pedigree (not just within family).
Correct current problems and rerun pedigreeCheck.
There may be additional problems not investigated because of the current problems.
All row numbers refer to row in the full pedigree (not just within family).
Correct current problems and rerun pedigreeCheck.
There may be additional problems not investigated because of the current problems.
All row numbers refer to row in the full pedigree (not just within family).
Correct current problems and rerun pedigreeCheck.
There may be additional problems not investigated because of the current problems.
subject 1 out of 34, 2 replications
subject 2 out of 34, 2 replications
subject 3 out of 34, 2 replications
subject 4 out of 34, 2 replications
subject 5 out of 34, 2 replications
subject 6 out of 34, 2 replications
subject 7 out of 34, 2 replications
subject 8 out of 34, 2 replications
subject 9 out of 34, 2 replications
subject 10 out of 34, 2 replications
subject 11 out of 34, 2 replications
subject 12 out of 34, 2 replications
subject 13 out of 34, 2 replications
subject 14 out of 34, 2 replications
subject 15 out of 34, 2 replications
subject 16 out of 34, 2 replications
subject 17 out of 34, 2 replications
subject 18 out of 34, 2 replications
subject 19 out of 34, 2 replications
subject 20 out of 34, 2 replications
subject 21 out of 34, 2 replications
subject 22 out of 34, 2 replications
subject 23 out of 34, 2 replications
subject 24 out of 34, 2 replications
subject 25 out of 34, 2 replications
subject 26 out of 34, 2 replications
subject 27 out of 34, 2 replications
subject 28 out of 34, 2 replications
subject 29 out of 34, 2 replications
subject 30 out of 34, 2 replications
subject 31 out of 34, 2 replications
subject 32 out of 34, 2 replications
subject 33 out of 34, 2 replications
subject 34 out of 34, 2 replications
Preparing data structures...
Wed Jan 8 22:00:38 2025 [ 1 ] family: 4, child: 200047857, 1
Wed Jan 8 22:00:38 2025 [ 2 ] family: 4, child: 200047857, 2
Wed Jan 8 22:00:38 2025 [ 3 ] family: 4, child: 200047857, 3
Wed Jan 8 22:00:38 2025 [ 4 ] family: 4, child: 200047857, 4
Wed Jan 8 22:00:38 2025 [ 5 ] family: 5, child: 200102386, 1
Wed Jan 8 22:00:38 2025 [ 6 ] family: 5, child: 200102386, 2
Wed Jan 8 22:00:38 2025 [ 7 ] family: 5, child: 200102386, 3
Wed Jan 8 22:00:38 2025 [ 8 ] family: 5, child: 200102386, 4
Wed Jan 8 22:00:38 2025 [ 9 ] family: 5, child: 200102386, 5
Wed Jan 8 22:00:38 2025 [ 10 ] family: 5, child: 200102386, 6
Wed Jan 8 22:00:38 2025 [ 11 ] family: 5, child: 200102386, 7
Wed Jan 8 22:00:38 2025 [ 12 ] family: 5, child: 200102386, 8
Wed Jan 8 22:00:38 2025 [ 13 ] family: 9, child: 200066330, 1
Wed Jan 8 22:00:38 2025 [ 14 ] family: 9, child: 200066330, 2
Wed Jan 8 22:00:38 2025 [ 15 ] family: 9, child: 200066330, 3
Wed Jan 8 22:00:38 2025 [ 16 ] family: 9, child: 200066330, 4
Wed Jan 8 22:00:38 2025 [ 17 ] family: 12, child: 200013233, 1
Wed Jan 8 22:00:38 2025 [ 18 ] family: 12, child: 200013233, 2
Wed Jan 8 22:00:38 2025 [ 19 ] family: 12, child: 200013233, 3
Wed Jan 8 22:00:38 2025 [ 20 ] family: 12, child: 200013233, 4
Wed Jan 8 22:00:38 2025 [ 21 ] family: 28, child: 200034659, 1
Wed Jan 8 22:00:38 2025 [ 22 ] family: 28, child: 200034659, 2
Wed Jan 8 22:00:38 2025 [ 23 ] family: 28, child: 200034659, 3
Wed Jan 8 22:00:38 2025 [ 24 ] family: 28, child: 200034659, 4
Wed Jan 8 22:00:38 2025 [ 25 ] family: 1334, child: 200016815, 1
Wed Jan 8 22:00:38 2025 [ 26 ] family: 1334, child: 200016815, 2
Wed Jan 8 22:00:38 2025 [ 27 ] family: 1334, child: 200016815, 3
Wed Jan 8 22:00:38 2025 [ 28 ] family: 1334, child: 200016815, 4
Wed Jan 8 22:00:38 2025 [ 29 ] family: 1334, child: 200016815, 5
Wed Jan 8 22:00:38 2025 [ 30 ] family: 1334, child: 200016815, 6
Wed Jan 8 22:00:38 2025 [ 31 ] family: 1334, child: 200016815, 7
Wed Jan 8 22:00:38 2025 [ 32 ] family: 1334, child: 200016815, 8
Wed Jan 8 22:00:38 2025 [ 33 ] family: 1340, child: 200076256, 1
Wed Jan 8 22:00:38 2025 [ 34 ] family: 1340, child: 200076256, 2
Wed Jan 8 22:00:38 2025 [ 35 ] family: 1340, child: 200076256, 3
Wed Jan 8 22:00:38 2025 [ 36 ] family: 1340, child: 200076256, 4
Wed Jan 8 22:00:38 2025 [ 37 ] family: 1341, child: 200015835, 1
Wed Jan 8 22:00:38 2025 [ 38 ] family: 1341, child: 200015835, 2
Wed Jan 8 22:00:38 2025 [ 39 ] family: 1341, child: 200030290, 1
Wed Jan 8 22:00:38 2025 [ 40 ] family: 1341, child: 200030290, 2
Wed Jan 8 22:00:38 2025 [ 41 ] family: 1341, child: 200030290, 3
Wed Jan 8 22:00:38 2025 [ 42 ] family: 1341, child: 200030290, 4
Wed Jan 8 22:00:38 2025 [ 43 ] family: 1341, child: 200030290, 5
Wed Jan 8 22:00:38 2025 [ 44 ] family: 1341, child: 200030290, 6
Wed Jan 8 22:00:38 2025 [ 45 ] family: 1341, child: 200030290, 7
Wed Jan 8 22:00:38 2025 [ 46 ] family: 1341, child: 200030290, 8
Wed Jan 8 22:00:38 2025 [ 47 ] family: 1344, child: 200071490, 1
Wed Jan 8 22:00:38 2025 [ 48 ] family: 1344, child: 200071490, 2
Wed Jan 8 22:00:38 2025 [ 49 ] family: 1344, child: 200071490, 3
Wed Jan 8 22:00:38 2025 [ 50 ] family: 1344, child: 200071490, 4
Wed Jan 8 22:00:38 2025 [ 51 ] family: 1344, child: 200071490, 5
Wed Jan 8 22:00:38 2025 [ 52 ] family: 1344, child: 200071490, 6
Wed Jan 8 22:00:38 2025 [ 53 ] family: 1344, child: 200071490, 7
Wed Jan 8 22:00:38 2025 [ 54 ] family: 1344, child: 200071490, 8
Wed Jan 8 22:00:38 2025 [ 55 ] family: 1347, child: 200121301, 1
Wed Jan 8 22:00:38 2025 [ 56 ] family: 1347, child: 200121301, 2
Wed Jan 8 22:00:38 2025 [ 57 ] family: 1347, child: 200121301, 3
Wed Jan 8 22:00:38 2025 [ 58 ] family: 1347, child: 200121301, 4
Wed Jan 8 22:00:38 2025 [ 59 ] family: 1347, child: 200121301, 5
Wed Jan 8 22:00:38 2025 [ 60 ] family: 1347, child: 200121301, 6
Wed Jan 8 22:00:38 2025 [ 61 ] family: 1347, child: 200121301, 7
Wed Jan 8 22:00:38 2025 [ 62 ] family: 1347, child: 200121301, 8
Wed Jan 8 22:00:38 2025 [ 63 ] family: 1362, child: 200003297, 1
Wed Jan 8 22:00:38 2025 [ 64 ] family: 1362, child: 200003297, 2
Wed Jan 8 22:00:38 2025 [ 65 ] family: 1362, child: 200003297, 3
Wed Jan 8 22:00:38 2025 [ 66 ] family: 1362, child: 200003297, 4
Wed Jan 8 22:00:38 2025 [ 67 ] family: 1362, child: 200024383, 1
Wed Jan 8 22:00:38 2025 [ 68 ] family: 1362, child: 200024383, 2
Wed Jan 8 22:00:38 2025 [ 69 ] family: 1362, child: 200024383, 3
Wed Jan 8 22:00:38 2025 [ 70 ] family: 1362, child: 200024383, 4
Wed Jan 8 22:00:38 2025 [ 71 ] family: 1362, child: 200024383, 5
Wed Jan 8 22:00:38 2025 [ 72 ] family: 1362, child: 200024383, 6
Wed Jan 8 22:00:38 2025 [ 73 ] family: 1362, child: 200024383, 7
Wed Jan 8 22:00:38 2025 [ 74 ] family: 1362, child: 200024383, 8
Wed Jan 8 22:00:38 2025 [ 75 ] family: 1408, child: 200074814, 1
Wed Jan 8 22:00:38 2025 [ 76 ] family: 1408, child: 200074814, 2
Wed Jan 8 22:00:38 2025 [ 77 ] family: 1408, child: 200074814, 3
Wed Jan 8 22:00:38 2025 [ 78 ] family: 1408, child: 200074814, 4
Wed Jan 8 22:00:38 2025 [ 79 ] family: 1408, child: 200074814, 5
Wed Jan 8 22:00:38 2025 [ 80 ] family: 1408, child: 200074814, 6
Wed Jan 8 22:00:38 2025 [ 81 ] family: 1408, child: 200074814, 7
Wed Jan 8 22:00:38 2025 [ 82 ] family: 1408, child: 200074814, 8
Averaging over duplicate trios...
start time = 2025-01-08 22:00:39.168979
plot number = 1 system time = 2025-01-08 22:00:39.17082
plot number = 2 system time = 2025-01-08 22:00:39.188099
plot number = 3 system time = 2025-01-08 22:00:39.205342
plot number = 4 system time = 2025-01-08 22:00:39.222513
plot number = 5 system time = 2025-01-08 22:00:39.239668
plot number = 6 system time = 2025-01-08 22:00:39.256809
plot number = 7 system time = 2025-01-08 22:00:39.273992
plot number = 8 system time = 2025-01-08 22:00:39.291475
plot number = 9 system time = 2025-01-08 22:00:39.30885
Beginning Calculations...
Block 1 of 1 Completed - 0.006945 secs
Beginning Calculations...
Block 1 of 1 Completed - 0.003202 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.1668 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.1592 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.1624 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.03618 secs
Reading in Phenotype and Covariate Data...
Running analysis with 24 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.009742 secs
Reading in Phenotype and Covariate Data...
Running analysis with 42 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.03528 secs
start time = 2025-01-08 22:00:40.548591
plot number = 1 system time = 2025-01-08 22:00:40.550046
plot number = 2 system time = 2025-01-08 22:00:40.566885
plot number = 3 system time = 2025-01-08 22:00:40.583727
plot number = 4 system time = 2025-01-08 22:00:40.600555
plot number = 5 system time = 2025-01-08 22:00:40.617468
plot number = 6 system time = 2025-01-08 22:00:40.634395
plot number = 7 system time = 2025-01-08 22:00:40.651176
plot number = 8 system time = 2025-01-08 22:00:40.667894
plot number = 9 system time = 2025-01-08 22:00:40.684689
--- finished re-building ‘DataCleaning.Rnw’
--- re-building ‘Formats.Rnw’ using Sweave
--- finished re-building ‘Formats.Rnw’
SUMMARY: processing the following file failed:
‘Affymetrix.Rmd’
Error: Vignette re-building failed.
Execution halted