Laurent Gatto
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/pRoloc |
| git_branch: devel |
| git_last_commit: 69cdf26 |
| git_last_commit_date: 2024-04-30 10:29:44 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:17 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1563/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pRoloc 1.45.0 (landing page) Laurent Gatto
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the pRoloc 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: pRoloc |
| Version: 1.45.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pRoloc_1.45.0.tar.gz |
| StartedAt: 2024-05-19 22:52:02 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 23:02:41 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 638.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pRoloc.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pRoloc_1.45.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/pRoloc.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pRoloc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRoloc’ version ‘1.45.0’
* 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 ‘pRoloc’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
':::' calls which should be '::':
‘MLInterfaces:::.macroF1’ ‘MLInterfaces:::.precision’
‘MLInterfaces:::.recall’ ‘MLInterfaces:::es2df’
See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘caret:::predict.plsda’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘getAttributesOfInterest0’ ‘getAttributesOfInterestX’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘pRoloc/R/annotation.R’:
unlockBinding("params", .pRolocEnv)
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SpatProtVis-class 11.438 0.176 11.620
perTurboClassification 10.730 0.161 10.892
rfClassification 8.421 0.257 8.683
nnetClassification 5.832 0.034 5.866
ClustDist-class 5.460 0.220 6.247
ClustDistList-class 5.293 0.163 5.808
svmClassification 4.934 0.165 5.102
clustDist 4.607 0.178 5.140
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/pRoloc.Rcheck/00check.log’
for details.
pRoloc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pRoloc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘pRoloc’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dmvtCpp.cpp -o dmvtCpp.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pRoloc.cpp -o pRoloc.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o pRoloc.so RcppExports.o dmvtCpp.o pRoloc.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-pRoloc/00new/pRoloc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pRoloc)
pRoloc.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "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.
>
> # The setting of R_TESTS exists to work around an R bug. See
> # https://github.com/hadley/testthat/issues/144
> # We should remove it when the issue is resolved.
> Sys.setenv("R_TESTS" = "")
>
> library("testthat")
> library("pRoloc")
Loading required package: MSnbase
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, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
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: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.31.1
Visit https://lgatto.github.io/MSnbase/ to get started.
Consider switching to the 'R for Mass Spectrometry'
packages - see https://RforMassSpectrometry.org for details.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: XML
Attaching package: 'annotate'
The following object is masked from 'package:mzR':
nChrom
Loading required package: cluster
Loading required package: BiocParallel
This is pRoloc version 1.45.0
Visit https://lgatto.github.io/pRoloc/ to get started.
> library("pRolocdata")
This is pRolocdata version 1.41.0.
Use 'pRolocdata()' to list available data sets.
>
> test_check("pRoloc")
Object of class "SpatProtVis"
Data: dunkley2006
Visualisation methods: PCA, MDS, kpca
Done.
Connecting to Biomart...
Object of class "AnnotationParams"
Using the 'ENSEMBL_MART_ENSEMBL' BioMart database
Using the 'hsapiens_gene_ensembl' dataset
Using 'uniprotswissprot' as filter
Created on Sun May 19 23:00:55 2024
GO Term Evidence Code
Experimental Evidence Codes
EXP: Inferred from Experiment
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
Computational Analysis Evidence Codes
ISS: Inferred from Sequence or Structural Similarity
ISO: Inferred from Sequence Orthology
ISA: Inferred from Sequence Alignment
ISM: Inferred from Sequence Model
IGC: Inferred from Genomic Context
IBA: Inferred from Biological aspect of Ancestor
IBD: Inferred from Biological aspect of Descendant
IKR: Inferred from Key Residues
IRD: Inferred from Rapid Divergence
RCA: inferred from Reviewed Computational Analysis
Author Statement Evidence Codes
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
Curator Statement Evidence Codes
IC: Inferred by Curator
ND: No biological Data available
Automatically-assigned Evidence Codes
IEA: Inferred from Electronic Annotation
Obsolete Evidence Codes
NR: Not Recorded
Connecting to Biomart...
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5
3 2 3 1 1
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5
5 2 1 1 1
organelleMarkers
ORG1 unknown
3 7
organelleMarkers
ORG1 unknown
2 8
[1] "markers"
[1] "xx"
[1] "markers"
[1] "xx"
[1] "markers"
[1] "xx"
[1] "markers"
# weights: 269
initial value 666.839513
iter 10 value 207.573433
iter 20 value 34.513121
iter 30 value 1.438035
iter 40 value 0.496168
iter 50 value 0.419018
iter 60 value 0.386372
iter 70 value 0.360129
iter 80 value 0.324298
iter 90 value 0.294123
iter 100 value 0.252996
final value 0.252996
stopped after 100 iterations
[1] "xx"
# weights: 269
initial value 666.839513
iter 10 value 207.573433
iter 20 value 34.513121
iter 30 value 1.438035
iter 40 value 0.496168
iter 50 value 0.419018
iter 60 value 0.386372
iter 70 value 0.360129
iter 80 value 0.324298
iter 90 value 0.294123
iter 100 value 0.252996
final value 0.252996
stopped after 100 iterations
[1] "markers"
[1] "xx"
[1] "pd.markers"
Common markers: 0
Unique x markers: 49
Unique y markers: 34
Common unkowns: 11
Unique x unknowns: 40
Unique y unknowns: 66
my
mx ER lumen ER membrane Golgi Mitochondrion PM Plastid Ribosome
ER lumen 14 0 0 0 0 0 0
ER membrane 0 45 0 0 0 0 0
Golgi 0 0 28 0 0 0 0
Mitochondrion 0 0 0 55 0 0 0
PM 0 0 0 0 46 0 0
Plastid 0 0 0 0 0 20 0
Ribosome 0 0 0 0 0 0 19
TGN 0 0 0 0 0 0 0
unknown 0 0 0 0 0 0 0
vacuole 0 0 0 0 0 0 0
my
mx TGN unknown vacuole
ER lumen 0 0 0
ER membrane 0 0 0
Golgi 0 0 0
Mitochondrion 0 0 0
PM 0 0 0
Plastid 0 0 0
Ribosome 0 0 0
TGN 13 0 0
unknown 0 428 0
vacuole 0 0 21
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 146 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 146 ]
>
> proc.time()
user system elapsed
127.523 4.165 133.378
pRoloc.Rcheck/pRoloc-Ex.timings
| name | user | system | elapsed | |
| AnnotationParams-class | 0.289 | 0.032 | 1.080 | |
| ClustDist-class | 5.460 | 0.220 | 6.247 | |
| ClustDistList-class | 5.293 | 0.163 | 5.808 | |
| GenRegRes-class | 0.002 | 0.001 | 0.002 | |
| QSep-class | 0.407 | 0.029 | 0.437 | |
| SpatProtVis-class | 11.438 | 0.176 | 11.620 | |
| addGoAnnotations | 3.218 | 0.165 | 3.695 | |
| addMarkers | 0.167 | 0.006 | 0.175 | |
| checkFeatureNamesOverlap | 0.248 | 0.017 | 0.267 | |
| checkFvarOverlap | 0.033 | 0.006 | 0.039 | |
| chi2-methods | 0.001 | 0.001 | 0.002 | |
| classWeights | 0.117 | 0.009 | 0.127 | |
| clustDist | 4.607 | 0.178 | 5.140 | |
| empPvalues | 0.062 | 0.000 | 0.066 | |
| fDataToUnknown | 0.060 | 0.005 | 0.085 | |
| filterBinMSnSet | 0.157 | 0.003 | 0.172 | |
| filterZeroCols | 0.110 | 0.009 | 0.119 | |
| getGOFromFeatures | 0.386 | 0.043 | 0.429 | |
| getMarkerClasses | 0.042 | 0.006 | 0.051 | |
| getMarkers | 0.045 | 0.005 | 0.050 | |
| getPredictions | 0.261 | 0.024 | 0.284 | |
| getStockcol | 0.090 | 0.014 | 0.104 | |
| goIdToTerm | 2.124 | 0.080 | 2.204 | |
| highlightOnPlot | 0.415 | 0.018 | 0.435 | |
| knnClassification | 1.062 | 0.049 | 1.111 | |
| knntlClassification | 0 | 0 | 0 | |
| ksvmClassification | 4.196 | 0.119 | 4.330 | |
| makeGoSet | 0.794 | 0.051 | 0.848 | |
| markerMSnSet | 0.276 | 0.011 | 0.288 | |
| markers | 0.060 | 0.005 | 0.065 | |
| minMarkers | 0.050 | 0.005 | 0.054 | |
| mixing_posterior_check | 0.001 | 0.001 | 0.000 | |
| move2Ds | 2.689 | 0.096 | 2.790 | |
| mrkConsProfiles | 0.191 | 0.008 | 0.200 | |
| mrkHClust | 0.070 | 0.006 | 0.077 | |
| nbClassification | 2.090 | 0.039 | 2.130 | |
| nicheMeans2D | 0 | 0 | 0 | |
| nndist-methods | 0.211 | 0.010 | 0.221 | |
| nnetClassification | 5.832 | 0.034 | 5.866 | |
| orgQuants | 0.183 | 0.007 | 0.190 | |
| pRolocmarkers | 0.016 | 0.003 | 0.020 | |
| perTurboClassification | 10.730 | 0.161 | 10.892 | |
| phenoDisco | 0.000 | 0.000 | 0.001 | |
| plot2D | 4.331 | 0.108 | 4.450 | |
| plot2Ds | 0.425 | 0.060 | 0.498 | |
| plotConsProfiles | 0.409 | 0.009 | 0.419 | |
| plotDist | 0.173 | 0.012 | 0.185 | |
| plsdaClassification | 0 | 0 | 0 | |
| rfClassification | 8.421 | 0.257 | 8.683 | |
| sampleMSnSet | 0.061 | 0.005 | 0.066 | |
| showGOEvidenceCodes | 0.001 | 0.001 | 0.001 | |
| spatial2D | 0 | 0 | 0 | |
| svmClassification | 4.934 | 0.165 | 5.102 | |
| testMSnSet | 0.247 | 0.006 | 0.252 | |
| testMarkers | 0.035 | 0.005 | 0.040 | |
| thetas | 0.007 | 0.000 | 0.007 | |
| zerosInBinMSnSet | 3.880 | 0.105 | 3.986 | |