| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:45 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the Spectra package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1859/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Spectra 1.5.13 (landing page) RforMassSpectrometry Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Spectra |
| Version: 1.5.13 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Spectra.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Spectra_1.5.13.tar.gz |
| StartedAt: 2022-03-17 20:21:55 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:28:16 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 380.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Spectra.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Spectra.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Spectra_1.5.13.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Spectra.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Spectra/DESCRIPTION' ... OK
* this is package 'Spectra' version '1.5.13'
* 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 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 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 8.29 0.43 93.83
plotMzDelta 2.38 0.21 16.00
neutralLoss 0.50 0.04 6.08
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/Spectra.Rcheck/00check.log'
for details.
Spectra.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Spectra
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Spectra' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Spectra'
finding HTML links ... done
MsBackend html
finding level-2 HTML links ... done
MsBackendCached html
Spectra html
combinePeaks html
countIdentifications html
filterFourierTransformArtefacts html
hidden_aliases html
joinPeaks html
neutralLoss html
plotMzDelta html
spectra-plotting html
spectraVariableMapping html
*** 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)
Making 'packages.html' ... done
Spectra.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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 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
Attaching package: 'Spectra'
The following object is masked from 'package:ProtGenerics':
addProcessing
>
> 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_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
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
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
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
MSn data (Spectra) with 0 spectra in a MsBackendDataFrame backend:
Lazy evaluation queue: 2 processing step(s)
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
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
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
NULL
[ FAIL 0 | WARN 10 | SKIP 7 | PASS 1765 ]
== Skipped tests ===============================================================
* On CRAN (6)
* empty test (1)
[ FAIL 0 | WARN 10 | SKIP 7 | PASS 1765 ]
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
167.78 11.09 180.79
Spectra.Rcheck/Spectra-Ex.timings
| name | user | system | elapsed | |
| MsBackend | 0.13 | 0.02 | 0.14 | |
| Spectra | 8.29 | 0.43 | 93.83 | |
| combinePeaks | 0.03 | 0.00 | 0.03 | |
| countIdentifications | 0.33 | 0.02 | 3.29 | |
| filterFourierTransformArtefacts | 0.29 | 0.01 | 3.60 | |
| joinPeaks | 0.02 | 0.00 | 0.01 | |
| neutralLoss | 0.50 | 0.04 | 6.08 | |
| plotMzDelta | 2.38 | 0.21 | 16.00 | |
| spectra-plotting | 0.32 | 0.00 | 0.33 | |