| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:19 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 2019/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Spectra 1.12.0 (landing page) RforMassSpectrometry Package Maintainer
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the Spectra package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Spectra.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: Spectra |
| Version: 1.12.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Spectra.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Spectra_1.12.0.tar.gz |
| StartedAt: 2023-11-02 14:35:10 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 14:42:26 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 435.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Spectra.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Spectra.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Spectra_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Spectra.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Spectra/DESCRIPTION’ ... OK
* this is package ‘Spectra’ version ‘1.12.0’
* 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 ‘Spectra’ 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 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 ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("_H5Dclose", ..., PACKAGE = "rhdf5")
.Call("_H5Dopen", ..., PACKAGE = "rhdf5")
.Call("_H5Dread", ..., PACKAGE = "rhdf5")
.Call("_H5Fclose", ..., PACKAGE = "rhdf5")
.Call("_H5Fopen", ..., PACKAGE = "rhdf5")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotMzDelta 10.785 1.176 11.115
Spectra 9.025 1.583 8.627
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/Spectra.Rcheck/00check.log’
for details.
Spectra.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL Spectra ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘Spectra’ ... ** using staged installation ** R ** data ** inst ** 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 (Spectra)
Spectra.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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("patrick")
> library("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, setdiff, sort, 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
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
>
> register(SerialParam())
>
> sciex_file <- normalizePath(
+ dir(system.file("sciex", package = "msdata"), full.names = TRUE))
> cdf_file <- normalizePath(
+ dir(system.file("cdf", package = "msdata"), full.names = TRUE))
>
> sciex_mzr <- backendInitialize(MsBackendMzR(), files = sciex_file)
> sciex_pks <- peaksData(sciex_mzr)
> fl <- normalizePath(
+ dir(system.file("proteomics", package = "msdata"), full.names = TRUE))
> tmt_mzr <- backendInitialize(MsBackendMzR(), files = fl[5])
>
> fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML",
+ package = "msdata")
> sps_dia <- Spectra(fl)
>
> fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML",
+ package = "msdata")
> sps_dda <- Spectra(fl)
>
> sciex_hd5 <- backendInitialize(MsBackendHdf5Peaks(),
+ data = spectraData(sciex_mzr),
+ hdf5path = tempdir())
>
> test_suite <- system.file("test_backends", "test_MsBackend",
+ package = "Spectra")
> be <- sciex_mzr[1:10]
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
⠸ | 4 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠦ | 7 | spectra_subsetting
⠦ | 17 | spectra_subsetting
⠧ | 28 | spectra_subsetting
⠼ | 35 | spectra_subsetting
⠴ | 36 | spectra_subsetting
⠦ | 37 | spectra_subsetting
⠧ | 38 | spectra_subsetting
⠇ | 39 | spectra_subsetting
⠏ | 40 | spectra_subsetting
⠋ | 41 | spectra_subsetting
⠙ | 42 | spectra_subsetting
⠹ | 43 | spectra_subsetting
⠸ | 44 | spectra_subsetting
⠦ | 47 | spectra_subsetting
⠇ | 49 | spectra_subsetting
⠸ | 54 | spectra_subsetting
⠇ | 59 | spectra_subsetting
⠋ | 61 | spectra_subsetting
✔ | 61 | spectra_subsetting [2.1s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠼ | 25 | spectra_variables
⠋ | 31 | spectra_variables
⠸ | 44 | spectra_variables
⠸ | 54 | spectra_variables
✔ | 1 62 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.9 s
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_variables.R:262:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 127 ]
>
> be <- backendInitialize(MsBackendDataFrame(), spectraData(be))
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠼ | 5 | spectra_subsetting
⠹ | 13 | spectra_subsetting
⠏ | 20 | spectra_subsetting
⠧ | 28 | spectra_subsetting
⠼ | 35 | spectra_subsetting
⠏ | 40 | spectra_subsetting
⠴ | 46 | spectra_subsetting
⠹ | 53 | spectra_subsetting
⠧ | 58 | spectra_subsetting
✔ | 61 | spectra_subsetting [1.1s]
⠏ | 0 | spectra_variables
⠴ | 6 | spectra_variables
⠏ | 10 | spectra_variables
⠧ | 18 | spectra_variables
⠧ | 28 | spectra_variables
⠸ | 34 | spectra_variables
⠧ | 38 | spectra_variables
⠏ | 50 | spectra_variables
⠇ | 59 | spectra_variables
⠦ | 67 | spectra_variables
⠋ | 71 | spectra_variables
✔ | 78 | spectra_variables [1.2s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.4 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 143 ]
>
> be <- backendInitialize(MsBackendMemory(), spectraData(be))
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
⠸ | 4 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠸ | 14 | spectra_subsetting
⠙ | 32 | spectra_subsetting
⠸ | 34 | spectra_subsetting
⠧ | 38 | spectra_subsetting
⠹ | 43 | spectra_subsetting
⠏ | 50 | spectra_subsetting
⠦ | 57 | spectra_subsetting
✔ | 61 | spectra_subsetting [1.1s]
⠏ | 0 | spectra_variables
⠼ | 15 | spectra_variables
⠼ | 35 | spectra_variables
⠴ | 46 | spectra_variables
⠙ | 62 | spectra_variables
⠏ | 70 | spectra_variables
✔ | 80 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.9 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 145 ]
>
> ## be <- sciex_hd5[1:10]
> ## test_dir(test_suite, stop_on_failure = TRUE)
>
> test_check("Spectra")
Error in .h5_read_bare(fid, "/header/modcount") :
HDF5. Dataset. Can't open object.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) :
HDF5. File accessibility. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) :
HDF5. File accessibility. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) :
HDF5. File accessibility. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) :
HDF5. File accessibility. Unable to open file.
MsBackendHdf5Peaks with 3 spectra
msLevel rtime scanIndex
<integer> <numeric> <integer>
1 1 NA 1
2 2 NA 1
3 2 NA 2
... 16 more variables/columns.
file(s):
c
d
MsBackendMzR with 0 spectra
MsBackendMzR with 1862 spectra
msLevel rtime scanIndex
<integer> <numeric> <integer>
1 1 0.280 1
2 1 0.559 2
3 1 0.838 3
4 1 1.117 4
5 1 1.396 5
... ... ... ...
1858 1 258.636 927
1859 1 258.915 928
1860 1 259.194 929
1861 1 259.473 930
1862 1 259.752 931
... 33 more variables/columns.
file(s):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
MSn data (Spectra) with 0 spectra in a MsBackendMemory backend:
Lazy evaluation queue: 2 processing step(s)
MSn data (Spectra) with 1862 spectra in a MsBackendMzR backend:
msLevel rtime scanIndex
<integer> <numeric> <integer>
1 1 0.280 1
2 1 0.559 2
3 1 0.838 3
4 1 1.117 4
5 1 1.396 5
... ... ... ...
1858 1 258.636 927
1859 1 258.915 928
1860 1 259.194 929
1861 1 259.473 930
1862 1 259.752 931
... 33 more variables/columns.
file(s):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
NULL
[ FAIL 0 | WARN 7 | SKIP 7 | PASS 2549 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test_plotMzDelta.R:30:5', 'test_plotting-functions.R:17:5',
'test_plotting-functions.R:50:5', 'test_plotting-functions.R:69:5',
'test_plotting-functions.R:99:5', 'test_plotting-functions.R:144:5'
• empty test (1): 'test_MsBackendMzR.R:464:1'
[ FAIL 0 | WARN 7 | SKIP 7 | PASS 2549 ]
Deleting unused snapshots:
• plotting-functions/plot-single-spectrum-labels-ass.svg
• plotting-functions/plot-single-spectrum-labels.svg
• plotting-functions/plot-single-spectrum-xlim.svg
• plotting-functions/plotspectra-asp05.svg
• plotting-functions/plotspectra-asp2.svg
• plotting-functions/plotspectra-color-peaks-label-labelcol.svg
• plotting-functions/plotspectra-color-peaks-label.svg
• plotting-functions/plotspectra-color-peaks.svg
• plotting-functions/plotspectramirror-match-color-labelcol.svg
• plotting-functions/plotspectramirror-match-color.svg
• plotting-functions/plotspectramirror-same.svg
• plotting-functions/plotspectraoverlay-no-axes.svg
• plotting-functions/plotspectraoverlay-xlim.svg
>
> proc.time()
user system elapsed
306.578 5.866 312.339
Spectra.Rcheck/Spectra-Ex.timings
| name | user | system | elapsed | |
| MsBackend | 0.321 | 0.000 | 0.321 | |
| Spectra | 9.025 | 1.583 | 8.627 | |
| chunkapply | 0.648 | 0.116 | 0.766 | |
| combinePeaksData | 0.035 | 0.000 | 0.036 | |
| countIdentifications | 0.034 | 0.016 | 0.096 | |
| estimatePrecursorIntensity | 4.306 | 0.473 | 4.664 | |
| filterFourierTransformArtefacts | 0.057 | 0.016 | 0.074 | |
| joinPeaks | 0.004 | 0.000 | 0.004 | |
| neutralLoss | 0.293 | 0.043 | 0.337 | |
| plotMzDelta | 10.785 | 1.176 | 11.115 | |
| spectra-plotting | 0.308 | 0.048 | 0.357 | |