| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:34 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1982/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Spectra 1.10.3 (landing page) RforMassSpectrometry Package Maintainer
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: Spectra |
| Version: 1.10.3 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Spectra.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Spectra_1.10.3.tar.gz |
| StartedAt: 2023-10-16 07:27:46 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 07:40:58 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 791.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Spectra.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Spectra.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Spectra_1.10.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Spectra.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Spectra/DESCRIPTION’ ... OK
* this is package ‘Spectra’ version ‘1.10.3’
* 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 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
Spectra 18.425 4.224 25.073
plotMzDelta 14.104 1.359 18.314
* 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
‘/Users/biocbuild/bbs-3.17-bioc/meat/Spectra.Rcheck/00check.log’
for details.
Spectra.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Spectra ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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: x86_64-apple-darwin20 (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("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])
>
> 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 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠸ | 4 | spectra_subsetting
⠏ | 10 | spectra_subsetting
⠴ | 16 | spectra_subsetting
⠙ | 22 | spectra_subsetting
⠧ | 28 | spectra_subsetting
⠹ | 33 | 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
⠧ | 48 | spectra_subsetting
⠇ | 49 | spectra_subsetting
⠹ | 53 | spectra_subsetting
⠴ | 56 | spectra_subsetting
⠏ | 60 | spectra_subsetting
⠋ | 61 | spectra_subsetting
✔ | 61 | spectra_subsetting [4.4s]
⠏ | 0 | spectra_variables
⠙ | 2 | spectra_variables
⠏ | 10 | spectra_variables
⠸ | 14 | spectra_variables
⠙ | 22 | spectra_variables
⠧ | 28 | spectra_variables
⠙ | 32 | spectra_variables
⠋ | 41 | spectra_variables
⠧ | 48 | spectra_variables
⠸ | 54 | spectra_variables
⠇ | 1 58 | spectra_variables
✔ | 1 62 | spectra_variables [1.2s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 5.7 s
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_variables.R:262:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 123 ]
>
> be <- backendInitialize(MsBackendDataFrame(), spectraData(be))
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠦ | 7 | spectra_subsetting
⠋ | 11 | spectra_subsetting
⠴ | 16 | spectra_subsetting
⠇ | 19 | spectra_subsetting
⠹ | 23 | spectra_subsetting
⠧ | 28 | spectra_subsetting
⠙ | 32 | spectra_subsetting
⠸ | 34 | spectra_subsetting
⠴ | 36 | spectra_subsetting
⠇ | 39 | spectra_subsetting
⠙ | 42 | spectra_subsetting
⠴ | 46 | spectra_subsetting
⠏ | 50 | spectra_subsetting
⠹ | 53 | spectra_subsetting
⠴ | 56 | spectra_subsetting
⠇ | 59 | spectra_subsetting
✔ | 61 | spectra_subsetting [2.3s]
⠏ | 0 | spectra_variables
⠙ | 2 | spectra_variables
⠴ | 6 | spectra_variables
⠦ | 7 | spectra_variables
⠏ | 10 | spectra_variables
⠦ | 17 | spectra_variables
⠼ | 25 | spectra_variables
⠧ | 28 | spectra_variables
⠋ | 31 | spectra_variables
⠸ | 34 | spectra_variables
⠦ | 37 | spectra_variables
⠧ | 38 | spectra_variables
⠸ | 44 | spectra_variables
⠼ | 45 | spectra_variables
⠹ | 53 | spectra_variables
⠇ | 59 | spectra_variables
⠙ | 62 | spectra_variables
⠦ | 67 | spectra_variables
⠏ | 70 | spectra_variables
⠙ | 72 | spectra_variables
✔ | 78 | spectra_variables [2.8s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 5.1 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 139 ]
>
> be <- backendInitialize(MsBackendMemory(), spectraData(be))
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | spectra_subsetting
⠧ | 8 | spectra_subsetting
⠧ | 18 | spectra_subsetting
⠧ | 28 | spectra_subsetting
⠼ | 35 | spectra_subsetting
⠦ | 37 | spectra_subsetting
⠇ | 39 | spectra_subsetting
⠙ | 42 | spectra_subsetting
⠸ | 44 | spectra_subsetting
⠧ | 48 | spectra_subsetting
⠹ | 53 | spectra_subsetting
⠴ | 56 | spectra_subsetting
⠋ | 61 | spectra_subsetting
✔ | 61 | spectra_subsetting [1.4s]
⠏ | 0 | spectra_variables
⠧ | 8 | spectra_variables
⠦ | 17 | spectra_variables
⠴ | 26 | spectra_variables
⠴ | 36 | spectra_variables
⠧ | 38 | spectra_variables
⠧ | 48 | spectra_variables
⠸ | 54 | spectra_variables
⠹ | 63 | spectra_variables
⠏ | 70 | spectra_variables
⠇ | 79 | spectra_variables
✔ | 80 | spectra_variables [1.4s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.9 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 141 ]
>
> ## 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 2292 ]
══ 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 2292 ]
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
414.744 13.579 530.934
Spectra.Rcheck/Spectra-Ex.timings
| name | user | system | elapsed | |
| MsBackend | 0.506 | 0.013 | 0.693 | |
| Spectra | 18.425 | 4.224 | 25.073 | |
| chunkapply | 0.608 | 0.147 | 0.968 | |
| combinePeaks | 0.061 | 0.009 | 0.088 | |
| countIdentifications | 0.114 | 0.100 | 0.224 | |
| filterFourierTransformArtefacts | 0.098 | 0.028 | 0.154 | |
| joinPeaks | 0.007 | 0.008 | 0.019 | |
| neutralLoss | 0.474 | 0.073 | 0.679 | |
| plotMzDelta | 14.104 | 1.359 | 18.314 | |
| spectra-plotting | 0.596 | 0.118 | 0.921 | |