| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-29 16:34:05 -0000 (Sun, 29 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4021 |
| 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 phantasus package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/phantasus.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1455/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| phantasus 1.19.4 (landing page) Alexey Sergushichev
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: phantasus |
| Version: 1.19.4 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings phantasus_1.19.4.tar.gz |
| StartedAt: 2023-01-29 06:03:01 -0000 (Sun, 29 Jan 2023) |
| EndedAt: 2023-01-29 06:38:47 -0000 (Sun, 29 Jan 2023) |
| EllapsedTime: 2146.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: phantasus.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings phantasus_1.19.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/phantasus.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘phantasus/DESCRIPTION’ ... OK
* this is package ‘phantasus’ version ‘1.19.4’
* 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 ‘phantasus’ can be installed ... OK
* checking package 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Warning message:
In utils::packageDescription(basename(dir), dirname(dir)) :
no package 'phantasus' was found
* 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 ... WARNING
Error in library(phantasus, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘phantasus’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'GEOquery:::.parseGPLTxt' 'GEOquery:::getDirListing'
'opencpu:::rookhandler' 'opencpu:::tmp_root' 'opencpu:::win_or_mac'
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 ... NOTE
generatePreloadedSession: no visible binding for global variable 'es'
generatePreloadedSession: no visible binding for global variable
'heatmapJson'
getCountsMetaPart: no visible binding for global variable 'file_name'
loadCounts: no visible global function definition for '.'
loadCounts: no visible binding for global variable 'directory'
loadCounts: no visible binding for global variable 'DT_counts_meta'
loadCounts: no visible binding for global variable 'accession'
loadCounts: no visible binding for global variable 'collection_type'
loadCounts: no visible binding for global variable 'file_name'
loadSession: no visible binding for global variable 'es'
safeDownload: no visible binding for global variable 'tempDestFile'
validateCountsCollection: no visible binding for global variable
'file_name'
Undefined global functions or variables:
. DT_counts_meta accession collection_type directory es file_name
heatmapJson tempDestFile
* checking Rd files ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:36-41: Dropping empty section \examples
* 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 ... SKIPPED
* 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:
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─phantasus:::checkGSEType("GSE33356", tempdir())
5. └─base::sapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─phantasus (local) FUN(X[[i]], ...)
8. └─phantasus:::getBriefData(gpl, destdir = destDir)
9. └─httr::GET(url)
10. └─httr:::request_perform(req, hu$handle$handle)
11. ├─httr:::request_fetch(req$output, req$url, handle)
12. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
13. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 100 ]
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 ...
‘phantasus-tutorial.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/phantasus.Rcheck/00check.log’
for details.
phantasus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL phantasus ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘phantasus’ ... ** 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 (phantasus)
phantasus.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> library(phantasus)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading config from /home/biocbuild/bbs-3.17-bioc/R/site-library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.config/R/opencpu/user.conf
>
> test_check("phantasus")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107746/matrix/GSE107746_series_matrix.txt.gz'
Content type 'application/x-gzip' length 7196 bytes
==================================================
downloaded 7196 bytes
trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL20795&form=text&view=data'
downloaded 48 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS4nnn/GDS4885/soft/GDS4885.soft.gz'
Content type 'application/x-gzip' length 1250109 bytes (1.2 MB)
downloaded 16 KB
trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data'
downloaded 48 bytes
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 100 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testCollapse.R:64'): Collapse strip unannotated rows ────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
Backtrace:
▆
1. └─phantasus::getGSE("GSE53986") at testCollapse.R:64:4
2. └─phantasus:::checkGSEType(name, destdir)
3. └─base::sapply(...)
4. └─base::lapply(X = X, FUN = FUN, ...)
5. └─phantasus (local) FUN(X[[i]], ...)
6. └─phantasus:::getBriefData(gpl, destdir = destDir)
7. └─httr::GET(url)
8. └─httr:::request_perform(req, hu$handle$handle)
9. ├─httr:::request_fetch(req$output, req$url, handle)
10. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
11. └─curl::curl_fetch_memory(url, handle = handle)
── Error ('testloadGEO.R:11'): loadGEO finishes with result ────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [www.ncbi.nlm.nih.gov] Failed to connect to www.ncbi.nlm.nih.gov port 80 after 5203 ms: Connection timed out
Backtrace:
▆
1. └─phantasus:::loadGEO("GSE27112") at testloadGEO.R:11:4
2. └─phantasus::getES(name, type, destdir = cacheDir, mirrorPath = mirrorPath)
3. └─phantasus::getGSE(name, destdir, mirrorPath)
4. └─phantasus:::checkGSEType(name, destdir)
5. └─phantasus:::getBriefData(name, destDir)
6. └─httr::GET(url)
7. └─httr:::request_perform(req, hu$handle$handle)
8. ├─httr:::request_fetch(req$output, req$url, handle)
9. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
10. └─curl::curl_fetch_memory(url, handle = handle)
── Error ('testloadGEO.R:35'): getGDS adds id field for GDS datasets ───────────
Error in `curl::curl_download(url, destfile, mode = mode, quiet = quiet,
handle = h)`: Timeout was reached: [] Operation timed out after 120009 milliseconds with 49152 out of 1250109 bytes received
Backtrace:
▆
1. └─phantasus::getGDS("GDS4885") at testloadGEO.R:35:4
2. ├─base::suppressWarnings(...)
3. │ └─base::withCallingHandlers(...)
4. └─GEOquery::getGEO(GEO = name, destdir = fullGEODirPath, AnnotGPL = TRUE)
5. └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
6. └─GEOquery:::downloadFile(myurl, destfile, mode)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─value[[3L]](cond)
── Error ('testloadGEO.R:41'): filterPhenoAnnotations saves colnames ───────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
Backtrace:
▆
1. └─phantasus::getES("GSE53986", destdir = cacheDir) at testloadGEO.R:41:4
2. └─phantasus::getGSE(name, destdir, mirrorPath)
3. └─phantasus:::checkGSEType(name, destdir)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─phantasus (local) FUN(X[[i]], ...)
7. └─phantasus:::getBriefData(gpl, destdir = destDir)
8. └─httr::GET(url)
9. └─httr:::request_perform(req, hu$handle$handle)
10. ├─httr:::request_fetch(req$output, req$url, handle)
11. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
12. └─curl::curl_fetch_memory(url, handle = handle)
── Error ('testloadGEO.R:47'): reparseCachedGSEs works ─────────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
Backtrace:
▆
1. └─phantasus::getES("GSE14308", destdir = cacheDir) at testloadGEO.R:47:4
2. └─phantasus::getGSE(name, destdir, mirrorPath)
3. └─phantasus:::checkGSEType(name, destdir)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─phantasus (local) FUN(X[[i]], ...)
7. └─phantasus:::getBriefData(gpl, destdir = destDir)
8. └─httr::GET(url)
9. └─httr:::request_perform(req, hu$handle$handle)
10. ├─httr:::request_fetch(req$output, req$url, handle)
11. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
12. └─curl::curl_fetch_memory(url, handle = handle)
── Error ('testloadGEO.R:87'): getGSE works with ARCHS4 ────────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Error in the HTTP2 framing layer
Backtrace:
▆
1. └─phantasus::getGSE(...) at testloadGEO.R:87:4
2. └─phantasus:::checkGSEType(name, destdir)
3. └─base::sapply(...)
4. └─base::lapply(X = X, FUN = FUN, ...)
5. └─phantasus (local) FUN(X[[i]], ...)
6. └─phantasus:::getBriefData(gpl, destdir = destDir)
7. └─httr::GET(url)
8. └─httr:::request_perform(req, hu$handle$handle)
9. ├─httr:::request_fetch(req$output, req$url, handle)
10. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
11. └─curl::curl_fetch_memory(url, handle = handle)
── Error ('testloadGEO.R:134'): getGSEType works ───────────────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Error in the HTTP2 framing layer
Backtrace:
▆
1. ├─testthat::expect_true(checkGSEType("GSE33356", tempdir())) at testloadGEO.R:134:4
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─phantasus:::checkGSEType("GSE33356", tempdir())
5. └─base::sapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─phantasus (local) FUN(X[[i]], ...)
8. └─phantasus:::getBriefData(gpl, destdir = destDir)
9. └─httr::GET(url)
10. └─httr:::request_perform(req, hu$handle$handle)
11. ├─httr:::request_fetch(req$output, req$url, handle)
12. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
13. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 100 ]
Error: Test failures
Execution halted