| Back to Rapid builds (Linux only) of a subset of BioC 3.21 Report updated every 6 hours |
This page was generated on 2025-04-04 20:37 -0400 (Fri, 04 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 871 |
| 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 143/217 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| MsExperiment 1.9.1 (landing page) Laurent Gatto
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
|
To the developers/maintainers of the MsExperiment package: - 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: MsExperiment |
| Version: 1.9.1 |
| Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:MsExperiment.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings MsExperiment_1.9.1.tar.gz |
| StartedAt: 2025-04-04 20:08:09 -0400 (Fri, 04 Apr 2025) |
| EndedAt: 2025-04-04 20:12:02 -0400 (Fri, 04 Apr 2025) |
| EllapsedTime: 233.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MsExperiment.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:MsExperiment.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings MsExperiment_1.9.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsExperiment.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MsExperiment/DESCRIPTION’ ... OK
* this is package ‘MsExperiment’ version ‘1.9.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MsExperiment’ 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 code 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: ‘IRanges:::.showAtomicList’
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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MsExperiment-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbWriteSampleData
> ### Title: Write sample annotations to a MsBackendSql SQL database
> ### Aliases: dbWriteSampleData
>
> ### ** Examples
>
>
> library(MsExperiment)
>
> ## Create a MsBackendSql database from two mzML files.
> ## Connect first to an empty SQLite database (for the example we create
> ## a database in a temporary file).
> library(RSQLite)
> sqlite_db <- tempfile()
> con <- dbConnect(SQLite(), sqlite_db)
>
> ## Define the files from which we import the data
> fls <- dir(system.file("sciex", package = "msdata"), pattern = "mzML",
+ full.names = TRUE)
>
> ## Create a MsBackendSql database containing the full MS data
> library(MsBackendSql)
Loading required package: Spectra
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: BiocParallel
> createMsBackendSqlDatabase(con, fls)
Importing data ...
Error: database or disk is full
Error: no such savepoint: dbAppendTable_431759_loatcfjjfo
Error: no such savepoint: dbWriteTable_431759_ueiyneebjy
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MsExperiment 4.608 0.361 5.183
* 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:
15. ├─DBI::dbSendStatement(conn, statement, ...)
16. └─DBI::dbSendStatement(conn, statement, ...)
17. ├─DBI::dbSendQuery(conn, statement, ...)
18. └─RSQLite::dbSendQuery(conn, statement, ...)
19. └─RSQLite (local) .local(conn, statement, ...)
20. ├─methods::new(...)
21. │ ├─methods::initialize(value, ...)
22. │ └─methods::initialize(value, ...)
23. └─RSQLite:::result_create(conn@ptr, statement)
[ FAIL 6 | WARN 55 | SKIP 0 | PASS 230 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsExperiment.Rcheck/00check.log’
for details.
MsExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL MsExperiment ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘MsExperiment’ ... ** this is package ‘MsExperiment’ version ‘1.9.1’ ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (MsExperiment)
MsExperiment.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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("MsExperiment")
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
> library("msdata")
> library("S4Vectors")
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
> library("Spectra")
Loading required package: BiocParallel
>
> fls <- dir(system.file("sciex", package = "msdata"), pattern = "mzML",
+ full.names = TRUE)
>
> mse <- MsExperiment()
> df <- data.frame(sample = c("QC1", "QC2"),
+ time = c(1, 2),
+ mzML_file = basename(fls))
> sampleData(mse) <- DataFrame(df)
> experimentFiles(mse) <- MsExperimentFiles(mzML_file = fls,
+ other_file = "other_file.txt")
> spectra(mse) <- Spectra(fls)
>
> test_check("MsExperiment")
[ FAIL 6 | WARN 55 | SKIP 0 | PASS 230 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_MsExperiment-db.R:6:1'): (code run outside of `test_that()`) ───
Error: database or disk is full
Backtrace:
▆
1. ├─ProtGenerics::setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con) at test_MsExperiment-db.R:6:1
2. └─MsBackendSql (local) setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con)
3. └─MsBackendSql (local) .local(object, backend, ...)
4. └─MsBackendSql:::.set_backend_insert_data(...)
5. └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
6. ├─DBI::dbWriteTable(...)
7. └─RSQLite::dbWriteTable(...)
8. └─RSQLite (local) .local(conn, name, value, ...)
9. ├─DBI::dbAppendTable(conn = conn, name = name, value = value)
10. └─RSQLite::dbAppendTable(conn = conn, name = name, value = value)
11. ├─methods::callNextMethod()
12. └─DBI (local) .nextMethod(conn = conn, name = name, value = value)
13. ├─DBI::dbExecute(conn, query, params = unname(as.list(value)))
14. └─DBI::dbExecute(conn, query, params = unname(as.list(value)))
15. ├─DBI::dbSendStatement(conn, statement, ...)
16. └─DBI::dbSendStatement(conn, statement, ...)
17. ├─DBI::dbSendQuery(conn, statement, ...)
18. └─RSQLite::dbSendQuery(conn, statement, ...)
19. └─RSQLite (local) .local(conn, statement, ...)
20. ├─DBI::dbBind(rs, params)
21. └─RSQLite::dbBind(rs, params)
22. └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
23. └─RSQLite:::result_bind(res@ptr, params)
── Error ('test_MsExperiment-db.R:6:1'): (code run outside of `test_that()`) ───
Error: no such savepoint: dbAppendTable_433708_miknxixaiz
Backtrace:
▆
1. ├─ProtGenerics::setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con) at test_MsExperiment-db.R:6:1
2. └─MsBackendSql (local) setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con)
3. └─MsBackendSql (local) .local(object, backend, ...)
4. └─MsBackendSql:::.set_backend_insert_data(...)
5. └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
6. ├─DBI::dbWriteTable(...)
7. └─RSQLite::dbWriteTable(...)
8. └─RSQLite (local) .local(conn, name, value, ...)
9. ├─DBI::dbAppendTable(conn = conn, name = name, value = value)
10. └─RSQLite::dbAppendTable(conn = conn, name = name, value = value)
11. ├─DBI::dbRollback(conn, name = savepoint_id)
12. └─RSQLite::dbRollback(conn, name = savepoint_id)
13. └─RSQLite (local) .local(conn, ...)
14. ├─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
15. └─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
16. ├─DBI::dbSendStatement(conn, statement, ...)
17. └─DBI::dbSendStatement(conn, statement, ...)
18. ├─DBI::dbSendQuery(conn, statement, ...)
19. └─RSQLite::dbSendQuery(conn, statement, ...)
20. └─RSQLite (local) .local(conn, statement, ...)
21. ├─methods::new(...)
22. │ ├─methods::initialize(value, ...)
23. │ └─methods::initialize(value, ...)
24. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsExperiment-db.R:6:1'): (code run outside of `test_that()`) ───
Error: no such savepoint: dbWriteTable_433708_epnaouaoxc
Backtrace:
▆
1. ├─ProtGenerics::setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con) at test_MsExperiment-db.R:6:1
2. └─MsBackendSql (local) setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con)
3. └─MsBackendSql (local) .local(object, backend, ...)
4. └─MsBackendSql:::.set_backend_insert_data(...)
5. └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
6. ├─DBI::dbWriteTable(...)
7. └─RSQLite::dbWriteTable(...)
8. └─RSQLite (local) .local(conn, name, value, ...)
9. ├─DBI::dbRollback(conn, name = savepoint_id)
10. └─RSQLite::dbRollback(conn, name = savepoint_id)
11. └─RSQLite (local) .local(conn, ...)
12. ├─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
13. └─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
14. ├─DBI::dbSendStatement(conn, statement, ...)
15. └─DBI::dbSendStatement(conn, statement, ...)
16. ├─DBI::dbSendQuery(conn, statement, ...)
17. └─RSQLite::dbSendQuery(conn, statement, ...)
18. └─RSQLite (local) .local(conn, statement, ...)
19. ├─methods::new(...)
20. │ ├─methods::initialize(value, ...)
21. │ └─methods::initialize(value, ...)
22. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsExperiment.R:160:5'): MsExperiment works ─────────────────────
Error: database or disk is full
Backtrace:
▆
1. ├─ProtGenerics::setBackend(...) at test_MsExperiment.R:160:5
2. └─MsBackendSql (local) setBackend(...)
3. └─MsBackendSql (local) .local(object, backend, ...)
4. └─MsBackendSql:::.set_backend_insert_data(...)
5. └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
6. └─MsBackendSql:::.insert_spectra_variables(con, spd)
7. ├─DBI::dbWriteTable(...)
8. └─RSQLite::dbWriteTable(...)
9. └─RSQLite (local) .local(conn, name, value, ...)
10. ├─DBI::dbAppendTable(conn = conn, name = name, value = value)
11. └─RSQLite::dbAppendTable(conn = conn, name = name, value = value)
12. ├─methods::callNextMethod()
13. └─DBI (local) .nextMethod(conn = conn, name = name, value = value)
14. ├─DBI::dbExecute(conn, query, params = unname(as.list(value)))
15. └─DBI::dbExecute(conn, query, params = unname(as.list(value)))
16. ├─DBI::dbSendStatement(conn, statement, ...)
17. └─DBI::dbSendStatement(conn, statement, ...)
18. ├─DBI::dbSendQuery(conn, statement, ...)
19. └─RSQLite::dbSendQuery(conn, statement, ...)
20. └─RSQLite (local) .local(conn, statement, ...)
21. ├─DBI::dbBind(rs, params)
22. └─RSQLite::dbBind(rs, params)
23. └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
24. └─RSQLite:::result_bind(res@ptr, params)
── Error ('test_MsExperiment.R:160:5'): MsExperiment works ─────────────────────
Error: no such savepoint: dbAppendTable_433708_kmymdcjnsa
Backtrace:
▆
1. ├─ProtGenerics::setBackend(...) at test_MsExperiment.R:160:5
2. └─MsBackendSql (local) setBackend(...)
3. └─MsBackendSql (local) .local(object, backend, ...)
4. └─MsBackendSql:::.set_backend_insert_data(...)
5. └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
6. └─MsBackendSql:::.insert_spectra_variables(con, spd)
7. ├─DBI::dbWriteTable(...)
8. └─RSQLite::dbWriteTable(...)
9. └─RSQLite (local) .local(conn, name, value, ...)
10. ├─DBI::dbAppendTable(conn = conn, name = name, value = value)
11. └─RSQLite::dbAppendTable(conn = conn, name = name, value = value)
12. ├─DBI::dbRollback(conn, name = savepoint_id)
13. └─RSQLite::dbRollback(conn, name = savepoint_id)
14. └─RSQLite (local) .local(conn, ...)
15. ├─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
16. └─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
17. ├─DBI::dbSendStatement(conn, statement, ...)
18. └─DBI::dbSendStatement(conn, statement, ...)
19. ├─DBI::dbSendQuery(conn, statement, ...)
20. └─RSQLite::dbSendQuery(conn, statement, ...)
21. └─RSQLite (local) .local(conn, statement, ...)
22. ├─methods::new(...)
23. │ ├─methods::initialize(value, ...)
24. │ └─methods::initialize(value, ...)
25. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsExperiment.R:160:5'): MsExperiment works ─────────────────────
Error: no such savepoint: dbWriteTable_433708_mbtlzpcqrr
Backtrace:
▆
1. ├─ProtGenerics::setBackend(...) at test_MsExperiment.R:160:5
2. └─MsBackendSql (local) setBackend(...)
3. └─MsBackendSql (local) .local(object, backend, ...)
4. └─MsBackendSql:::.set_backend_insert_data(...)
5. └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
6. └─MsBackendSql:::.insert_spectra_variables(con, spd)
7. ├─DBI::dbWriteTable(...)
8. └─RSQLite::dbWriteTable(...)
9. └─RSQLite (local) .local(conn, name, value, ...)
10. ├─DBI::dbRollback(conn, name = savepoint_id)
11. └─RSQLite::dbRollback(conn, name = savepoint_id)
12. └─RSQLite (local) .local(conn, ...)
13. ├─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
14. └─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
15. ├─DBI::dbSendStatement(conn, statement, ...)
16. └─DBI::dbSendStatement(conn, statement, ...)
17. ├─DBI::dbSendQuery(conn, statement, ...)
18. └─RSQLite::dbSendQuery(conn, statement, ...)
19. └─RSQLite (local) .local(conn, statement, ...)
20. ├─methods::new(...)
21. │ ├─methods::initialize(value, ...)
22. │ └─methods::initialize(value, ...)
23. └─RSQLite:::result_create(conn@ptr, statement)
[ FAIL 6 | WARN 55 | SKIP 0 | PASS 230 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
MsExperiment.Rcheck/MsExperiment-Ex.timings
| name | user | system | elapsed | |
| MsExperiment | 4.608 | 0.361 | 5.183 | |
| MsExperimentFiles | 0.012 | 0.005 | 0.018 | |