| Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:39 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 1344/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendSql 1.4.0 (landing page) Johannes Rainer
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the MsBackendSql 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: MsBackendSql |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendSql_1.4.0.tar.gz |
| StartedAt: 2024-05-06 23:13:28 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 23:15:27 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 119.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendSql.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendSql_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/MsBackendSql.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendSql/DESCRIPTION’ ... OK
* this is package ‘MsBackendSql’ version ‘1.4.0’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
MsBackendSql.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendSql ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)
MsBackendSql.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, 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':
expand.grid, I, unname
Loading required package: BiocParallel
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
> 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 0s
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 0s
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 0s
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 27s
Creating indices .... Done
[1] TRUE
> tmt_be <- backendInitialize(MsBackendSql(), tmt_db)
>
> test_check("MsBackendSql")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 322 ]
>
> 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
⠙ | 2 | peaks_variables
⠸ | 4 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠏ | 80 | spectra_subsetting
⠦ | 187 | spectra_subsetting
⠦ | 287 | spectra_subsetting
⠋ | 391 | spectra_subsetting
⠏ | 500 | spectra_subsetting
⠇ | 599 | spectra_subsetting
⠹ | 603 | spectra_subsetting
⠦ | 607 | spectra_subsetting
⠋ | 611 | spectra_subsetting
⠼ | 615 | spectra_subsetting
⠇ | 619 | spectra_subsetting
⠹ | 623 | spectra_subsetting
⠼ | 625 | spectra_subsetting
⠧ | 628 | spectra_subsetting
⠙ | 632 | spectra_subsetting
⠴ | 636 | spectra_subsetting
⠏ | 640 | spectra_subsetting
⠸ | 644 | spectra_subsetting
⠧ | 648 | spectra_subsetting
⠙ | 652 | spectra_subsetting
⠴ | 656 | spectra_subsetting
⠏ | 660 | spectra_subsetting
⠸ | 664 | spectra_subsetting
⠧ | 668 | spectra_subsetting
⠙ | 672 | spectra_subsetting
⠴ | 676 | spectra_subsetting
⠏ | 680 | spectra_subsetting
⠸ | 684 | spectra_subsetting
⠧ | 688 | spectra_subsetting
⠙ | 692 | spectra_subsetting
⠴ | 696 | spectra_subsetting
⠏ | 700 | spectra_subsetting
⠸ | 704 | spectra_subsetting
⠧ | 708 | spectra_subsetting
⠙ | 712 | spectra_subsetting
⠴ | 716 | spectra_subsetting
⠏ | 720 | spectra_subsetting
⠸ | 724 | spectra_subsetting
⠧ | 728 | spectra_subsetting
⠙ | 732 | spectra_subsetting
⠴ | 736 | spectra_subsetting
⠏ | 740 | spectra_subsetting
⠸ | 744 | spectra_subsetting
⠧ | 748 | spectra_subsetting
⠙ | 752 | spectra_subsetting
⠴ | 756 | spectra_subsetting
⠏ | 760 | spectra_subsetting
⠸ | 764 | spectra_subsetting
⠧ | 768 | spectra_subsetting
⠙ | 772 | spectra_subsetting
⠴ | 776 | spectra_subsetting
⠇ | 779 | spectra_subsetting
⠙ | 782 | spectra_subsetting
⠴ | 786 | spectra_subsetting
⠏ | 790 | spectra_subsetting
⠸ | 794 | spectra_subsetting
⠏ | 800 | spectra_subsetting
⠹ | 813 | spectra_subsetting
✔ | 813 | spectra_subsetting [7.2s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠸ | 14 | spectra_variables
⠇ | 19 | spectra_variables
⠦ | 27 | spectra_variables
⠋ | 31 | spectra_variables
⠹ | 43 | spectra_variables
⠸ | 54 | spectra_variables
✔ | 64 | spectra_variables [1.0s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 8.5 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 881 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> be <- tmt_be[sample(seq_along(tmt_be), 300)]
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
⠙ | 2 | peaks_variables
⠸ | 4 | peaks_variables
✔ | 4 | peaks_variables [1.2s]
⠏ | 0 | spectra_subsetting
⠼ | 55 | spectra_subsetting
⠼ | 155 | spectra_subsetting
⠏ | 250 | spectra_subsetting
⠏ | 340 | spectra_subsetting
⠇ | 439 | spectra_subsetting
⠹ | 543 | spectra_subsetting
⠹ | 643 | spectra_subsetting
⠼ | 745 | spectra_subsetting
⠸ | 844 | spectra_subsetting
⠼ | 905 | spectra_subsetting
⠧ | 908 | spectra_subsetting
⠙ | 912 | spectra_subsetting
⠼ | 915 | spectra_subsetting
⠇ | 919 | spectra_subsetting
⠹ | 923 | spectra_subsetting
⠦ | 927 | spectra_subsetting
⠋ | 931 | spectra_subsetting
⠼ | 935 | spectra_subsetting
⠦ | 937 | spectra_subsetting
⠋ | 941 | spectra_subsetting
⠼ | 945 | spectra_subsetting
⠇ | 949 | spectra_subsetting
⠹ | 953 | spectra_subsetting
⠼ | 955 | spectra_subsetting
⠇ | 959 | spectra_subsetting
⠹ | 963 | spectra_subsetting
⠼ | 965 | spectra_subsetting
⠇ | 969 | spectra_subsetting
⠹ | 973 | spectra_subsetting
⠴ | 976 | spectra_subsetting
⠏ | 980 | spectra_subsetting
⠸ | 984 | spectra_subsetting
⠧ | 988 | spectra_subsetting
⠋ | 991 | spectra_subsetting
⠼ | 995 | spectra_subsetting
⠇ | 999 | spectra_subsetting
⠋ | 1001 | spectra_subsetting
⠼ | 1005 | spectra_subsetting
⠇ | 1009 | spectra_subsetting
⠹ | 1013 | spectra_subsetting
⠼ | 1015 | spectra_subsetting
⠇ | 1019 | spectra_subsetting
⠋ | 1021 | spectra_subsetting
⠼ | 1025 | spectra_subsetting
⠇ | 1029 | spectra_subsetting
⠹ | 1033 | spectra_subsetting
⠦ | 1037 | spectra_subsetting
⠋ | 1041 | spectra_subsetting
⠸ | 1044 | spectra_subsetting
⠦ | 1047 | spectra_subsetting
⠏ | 1050 | spectra_subsetting
⠸ | 1054 | spectra_subsetting
⠧ | 1058 | spectra_subsetting
⠙ | 1062 | spectra_subsetting
⠴ | 1066 | spectra_subsetting
⠏ | 1070 | spectra_subsetting
⠸ | 1074 | spectra_subsetting
⠧ | 1078 | spectra_subsetting
⠙ | 1082 | spectra_subsetting
⠴ | 1086 | spectra_subsetting
⠏ | 1090 | spectra_subsetting
⠸ | 1094 | spectra_subsetting
⠧ | 1098 | spectra_subsetting
⠙ | 1102 | spectra_subsetting
⠸ | 1104 | spectra_subsetting
⠧ | 1108 | spectra_subsetting
⠋ | 1111 | spectra_subsetting
⠼ | 1115 | spectra_subsetting
⠇ | 1119 | spectra_subsetting
⠹ | 1123 | spectra_subsetting
⠦ | 1127 | spectra_subsetting
⠋ | 1131 | spectra_subsetting
⠼ | 1135 | spectra_subsetting
⠧ | 1138 | spectra_subsetting
⠋ | 1141 | spectra_subsetting
⠸ | 1144 | spectra_subsetting
⠧ | 1148 | spectra_subsetting
⠏ | 1150 | spectra_subsetting
⠸ | 1154 | spectra_subsetting
⠴ | 1156 | spectra_subsetting
⠏ | 1160 | spectra_subsetting
⠸ | 1164 | spectra_subsetting
⠧ | 1168 | spectra_subsetting
⠙ | 1172 | spectra_subsetting
⠴ | 1176 | spectra_subsetting
⠏ | 1180 | spectra_subsetting
⠸ | 1184 | spectra_subsetting
⠧ | 1188 | spectra_subsetting
⠙ | 1192 | spectra_subsetting
⠴ | 1196 | spectra_subsetting
⠏ | 1200 | spectra_subsetting
⠸ | 1204 | spectra_subsetting
⠧ | 1218 | spectra_subsetting
⠋ | 1221 | spectra_subsetting
✔ | 1221 | spectra_subsetting [12.8s]
⠏ | 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 [4.4s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 18.4 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1289 ]
🎯 Your tests hit the mark 🎯
>
> dbDisconnect(mm8_db)
> dbDisconnect(mm8_db_blob)
> dbDisconnect(mm_db)
> dbDisconnect(tmt_db)
>
> proc.time()
user system elapsed
80.137 6.737 86.290
MsBackendSql.Rcheck/MsBackendSql-Ex.timings
| name | user | system | elapsed | |
| MsBackendSql | 1.352 | 0.169 | 1.518 | |