| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:16 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 2009/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Spectra 1.17.1 (landing page) RforMassSpectrometry Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | 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. |
| Package: Spectra |
| Version: 1.17.1 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Spectra.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Spectra_1.17.1.tar.gz |
| StartedAt: 2024-11-28 05:04:51 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 05:18:04 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 793.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Spectra.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Spectra.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Spectra_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Spectra.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Spectra/DESCRIPTION' ... OK
* this is package 'Spectra' version '1.17.1'
* 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 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 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 whether 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
MsBackend.Rd: bpparam, closest, SnowParam, NumericList
MsBackendCached.Rd: NumericList
Spectra.Rd: ProcessingStep-class, bpparam
addProcessing.Rd: bpparam, nentropy, common
combineSpectra.Rd: bpparam
compareSpectra.Rd: ndotproduct
estimatePrecursorIntensity.Rd: bpparam
estimatePrecursorMz.Rd: SerialParam
filterMsLevel.Rd: isotopologues, isotopicSubstitutionMatrix
joinPeaks.Rd: gnps
processingChunkSize.Rd: backendParallelFactor, bpparam
spectra-plotting.Rd: common
spectraData.Rd: bpparam, NumericList, SimpleList
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
addProcessing 13.80 1.08 26.61
filterMsLevel 7.70 0.66 13.61
compareSpectra 7.27 0.14 13.45
Spectra 3.64 0.34 35.34
plotMzDelta 2.83 0.17 19.82
combineSpectra 2.20 0.12 9.49
combinePeaks 1.70 0.11 46.01
spectraData 1.56 0.14 31.49
estimatePrecursorMz 0.78 0.04 116.03
estimatePrecursorIntensity 0.81 0.00 14.65
* 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: 2 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/Spectra.Rcheck/00check.log'
for details.
Spectra.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Spectra ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'Spectra' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'entropy' in package 'Spectra' ** 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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
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
>
> 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
⠙ | 2 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠦ | 7 | spectra_subsetting
⠇ | 19 | spectra_subsetting
⠋ | 31 | spectra_subsetting
⠼ | 35 | spectra_subsetting
⠦ | 37 | spectra_subsetting
⠇ | 39 | spectra_subsetting
⠋ | 41 | spectra_subsetting
⠹ | 43 | spectra_subsetting
⠸ | 44 | spectra_subsetting
⠦ | 47 | spectra_subsetting
⠋ | 51 | spectra_subsetting
⠏ | 60 | spectra_subsetting
⠹ | 63 | spectra_subsetting
⠧ | 68 | spectra_subsetting
✔ | 68 | spectra_subsetting [1.9s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠹ | 23 | spectra_variables
⠙ | 32 | spectra_variables
⠧ | 48 | spectra_variables
⠋ | 1 60 | spectra_variables
✔ | 1 62 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.6 s
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_variables.R:262:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 134 ]
>
> 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
⠸ | 4 | spectra_subsetting
⠹ | 13 | spectra_subsetting
⠙ | 22 | spectra_subsetting
⠏ | 30 | spectra_subsetting
⠼ | 35 | spectra_subsetting
⠋ | 41 | spectra_subsetting
⠦ | 47 | spectra_subsetting
⠴ | 56 | spectra_subsetting
⠸ | 64 | spectra_subsetting
✔ | 68 | spectra_subsetting [1.1s]
⠏ | 0 | spectra_variables
⠴ | 6 | spectra_variables
⠹ | 13 | spectra_variables
⠹ | 23 | spectra_variables
⠇ | 29 | spectra_variables
⠴ | 36 | spectra_variables
⠧ | 38 | spectra_variables
⠹ | 53 | spectra_variables
⠇ | 59 | spectra_variables
⠼ | 65 | spectra_variables
⠏ | 70 | spectra_variables
✔ | 78 | spectra_variables [1.2s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.4 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 150 ]
>
> be <- backendInitialize(MsBackendMemory(), spectraData(be))
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠹ | 23 | spectra_subsetting
⠴ | 36 | spectra_subsetting
⠋ | 41 | spectra_subsetting
⠧ | 48 | spectra_subsetting
⠹ | 63 | spectra_subsetting
✔ | 68 | spectra_subsetting
⠏ | 0 | spectra_variables
⠏ | 10 | spectra_variables
⠼ | 35 | spectra_variables
⠸ | 54 | spectra_variables
⠏ | 70 | spectra_variables
✔ | 80 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.4 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 152 ]
>
> ## 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 14 | SKIP 7 | PASS 2794 ]
══ 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 14 | SKIP 7 | PASS 2794 ]
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
299.96 17.00 346.98
Spectra.Rcheck/Spectra-Ex.timings
| name | user | system | elapsed | |
| MsBackend | 0.39 | 0.00 | 0.39 | |
| Spectra | 3.64 | 0.34 | 35.34 | |
| addProcessing | 13.80 | 1.08 | 26.61 | |
| chunkapply | 0.56 | 0.02 | 0.58 | |
| combinePeaks | 1.70 | 0.11 | 46.01 | |
| combinePeaksData | 0.05 | 0.00 | 0.05 | |
| combineSpectra | 2.20 | 0.12 | 9.49 | |
| compareSpectra | 7.27 | 0.14 | 13.45 | |
| countIdentifications | 0.33 | 0.02 | 4.69 | |
| estimatePrecursorIntensity | 0.81 | 0.00 | 14.65 | |
| estimatePrecursorMz | 0.78 | 0.04 | 116.03 | |
| filterFourierTransformArtefacts | 0.08 | 0.02 | 0.10 | |
| filterMsLevel | 7.70 | 0.66 | 13.61 | |
| filterPeaksRanges | 0.04 | 0.00 | 0.05 | |
| joinPeaks | 0.02 | 0.00 | 0.02 | |
| neutralLoss | 0.22 | 0.00 | 0.21 | |
| plotMzDelta | 2.83 | 0.17 | 19.82 | |
| spectra-plotting | 0.22 | 0.01 | 0.23 | |
| spectraData | 1.56 | 0.14 | 31.49 | |