Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1334/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendSql 1.6.0  (landing page)
Johannes Rainer
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/MsBackendSql
git_branch: RELEASE_3_20
git_last_commit: fdb2cd8
git_last_commit_date: 2024-10-29 11:17:06 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for MsBackendSql on teran2

To the developers/maintainers of the MsBackendSql package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendSql.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.

raw results


Summary

Package: MsBackendSql
Version: 1.6.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendSql_1.6.0.tar.gz
StartedAt: 2024-11-20 06:13:46 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 06:18:45 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 299.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendSql.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendSql_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/MsBackendSql.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendSql/DESCRIPTION’ ... OK
* this is package ‘MsBackendSql’ version ‘1.6.0’
* 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 ‘MsBackendSql’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK


Installation output

MsBackendSql.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MsBackendSql
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘MsBackendSql’ ...
** 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 (MsBackendSql)

Tests output

MsBackendSql.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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(MsBackendSql)
Loading required package: Spectra
Loading required package: S4Vectors
Loading required package: stats4
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


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
> library(Spectra)
> library(RSQLite)
> library(msdata)
> 
> mm8_file <- system.file("microtofq", "MM8.mzML", package = "msdata")
> mm8_sps <- Spectra(mm8_file)
> mm8_db <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm8_db, mm8_file, blob = FALSE)
Importing data ... 

[==========================================================] 1/1 (100%) in  1s
Creating indices .... Done
[1] TRUE
> mm8_be <- backendInitialize(MsBackendSql(), mm8_db)
> 
> mm8_db_blob <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm8_db_blob, mm8_file, blob = TRUE)
Importing data ... 

[==========================================================] 1/1 (100%) in  1s
Creating indices .... Done
[1] TRUE
> mm8_be_blob <- backendInitialize(MsBackendSql(), mm8_db_blob)
> 
> mm14_file <- system.file("microtofq", "MM14.mzML", package = "msdata")
> mm_db <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm_db, c(mm8_file, mm14_file), blob = FALSE)
Importing data ... 

[==========================================================] 1/1 (100%) in  1s
Creating indices .... Done
[1] TRUE
> mm_be <- backendInitialize(MsBackendSql(), mm_db)
> 
> tmt_file <- proteomics(full.names = TRUE)[4L]
> tmt_mzr <- backendInitialize(MsBackendMzR(), tmt_file)
> tmt_db <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(tmt_db, tmt_file, blob = FALSE)
Importing data ... 

[==========================================================] 1/1 (100%) in 40s
Creating indices .... Done
[1] TRUE
> tmt_be <- backendInitialize(MsBackendSql(), tmt_db)
> 
> test_check("MsBackendSql")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 367 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 367 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> test_suite <- system.file("test_backends", "test_MsBackend",
+                           package = "Spectra")
> 
> be <- mm8_be
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W  S  OK | Context

⠏ |          0 | peaks_variables                                                
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✔ |          4 | peaks_variables

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⠏ |          0 | spectra_variables                                              
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✔ |         64 | spectra_variables [1.8s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 21.8 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 888 ]

🌈 Your tests are over the rainbow 🌈
> 
> be <- tmt_be[sample(seq_along(tmt_be), 300)]
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W  S  OK | Context

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✔ |          4 | peaks_variables [2.3s]

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⠧ |        1128 | spectra_subsetting                                            
⠇ |        1129 | spectra_subsetting                                            
⠋ |        1131 | spectra_subsetting                                            
⠹ |        1133 | spectra_subsetting                                            
⠸ |        1134 | spectra_subsetting                                            
⠴ |        1136 | spectra_subsetting                                            
⠧ |        1138 | spectra_subsetting                                            
⠏ |        1140 | spectra_subsetting                                            
⠙ |        1142 | spectra_subsetting                                            
⠸ |        1144 | spectra_subsetting                                            
⠴ |        1146 | spectra_subsetting                                            
⠧ |        1148 | spectra_subsetting                                            
⠇ |        1149 | spectra_subsetting                                            
⠋ |        1151 | spectra_subsetting                                            
⠹ |        1153 | spectra_subsetting                                            
⠼ |        1155 | spectra_subsetting                                            
⠦ |        1157 | spectra_subsetting                                            
⠇ |        1159 | spectra_subsetting                                            
⠋ |        1161 | spectra_subsetting                                            
⠹ |        1163 | spectra_subsetting                                            
⠼ |        1165 | spectra_subsetting                                            
⠴ |        1166 | spectra_subsetting                                            
⠧ |        1168 | spectra_subsetting                                            
⠏ |        1170 | spectra_subsetting                                            
⠙ |        1172 | spectra_subsetting                                            
⠹ |        1173 | spectra_subsetting                                            
⠸ |        1174 | spectra_subsetting                                            
⠴ |        1176 | spectra_subsetting                                            
⠧ |        1178 | spectra_subsetting                                            
⠏ |        1180 | spectra_subsetting                                            
⠙ |        1182 | spectra_subsetting                                            
⠹ |        1183 | spectra_subsetting                                            
⠼ |        1185 | spectra_subsetting                                            
⠦ |        1187 | spectra_subsetting                                            
⠇ |        1189 | spectra_subsetting                                            
⠏ |        1190 | spectra_subsetting                                            
⠋ |        1191 | spectra_subsetting                                            
⠹ |        1193 | spectra_subsetting                                            
⠸ |        1194 | spectra_subsetting                                            
⠴ |        1196 | spectra_subsetting                                            
⠧ |        1198 | spectra_subsetting                                            
⠏ |        1200 | spectra_subsetting                                            
⠙ |        1202 | spectra_subsetting                                            
⠸ |        1204 | spectra_subsetting                                            
⠧ |        1208 | spectra_subsetting                                            
⠋ |        1221 | spectra_subsetting                                            
⠧ |        1228 | spectra_subsetting                                            
✔ |        1228 | spectra_subsetting [36.2s]

⠏ |          0 | spectra_variables                                              
⠙ |         12 | spectra_variables                                              
⠸ |         14 | spectra_variables                                              
⠴ |         16 | spectra_variables                                              
⠦ |         27 | spectra_variables                                              
⠇ |         29 | spectra_variables                                              
⠋ |         31 | spectra_variables                                              
⠹ |         43 | spectra_variables                                              
⠸ |         54 | spectra_variables                                              
✔ |         64 | spectra_variables [10.8s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 49.3 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1296 ]
> 
> dbDisconnect(mm8_db)
> dbDisconnect(mm8_db_blob)
> dbDisconnect(mm_db)
> dbDisconnect(tmt_db)
> 
> proc.time()
   user  system elapsed 
141.570  13.152 165.992 

Example timings

MsBackendSql.Rcheck/MsBackendSql-Ex.timings

nameusersystemelapsed
MsBackendSql2.4690.3153.342