Luyi Tian
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/scPipe |
| Branch: RELEASE_3_7 |
| Last Commit: 19a1726 |
| Last Changed Date: 2018-05-31 19:42:56 -0400 (Thu, 31 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:59:00 -0400 (Wed, 17 Oct 2018).
| Package 1332/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scPipe 1.2.1 Luyi Tian
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: scPipe |
| Version: 1.2.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scPipe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scPipe_1.2.1.tar.gz |
| StartedAt: 2018-10-16 23:58:07 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-17 00:02:12 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 244.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scPipe.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scPipe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scPipe_1.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/scPipe.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scPipe’ version ‘1.2.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘scPipe’ 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 ... WARNING
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/libs/Rhtslib.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/libs/Rhtslib.so, 6): Symbol not found: _lzma_easy_buffer_encode
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/libs/Rhtslib.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/libs/Rhtslib.so
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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 ... OK
* checking R code for possible problems ... NOTE
plot_demultiplex: no visible binding for global variable ‘status’
plot_demultiplex: no visible binding for global variable ‘count’
plot_demultiplex: no visible binding for global variable ‘label_y’
plot_demultiplex: no visible binding for global variable ‘label_tx’
Undefined global functions or variables:
count label_tx label_y status
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/scPipe/libs/scPipe.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_putchar’, possibly from ‘putchar’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘_srand48’, possibly from ‘srand48’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sc_sample_data 10.111 0.047 10.280
plot_QC_pairs 9.496 0.068 9.647
calculate_QC_metrics 0.859 0.096 10.035
* 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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/scPipe.Rcheck/00check.log’
for details.
scPipe.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scPipe
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘scPipe’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Gene.cpp -o Gene.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Interval.cpp -o Interval.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cellbarcode.cpp -o cellbarcode.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c detect_barcode.cpp -o detect_barcode.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c parsebam.cpp -o parsebam.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c parsecount.cpp -o parsecount.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_init' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
__KSEQ_BASIC(SCOPE, type_t) \
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:170:16: note: expanded from macro '__KSEQ_BASIC'
SCOPE kseq_t *kseq_init(type_t fd) \
^
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_destroy' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
__KSEQ_BASIC(SCOPE, type_t) \
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:176:13: note: expanded from macro '__KSEQ_BASIC'
SCOPE void kseq_destroy(kseq_t *ks) \
^
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_read' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:242:2: note: expanded from macro 'KSEQ_INIT2'
__KSEQ_READ(SCOPE)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:190:12: note: expanded from macro '__KSEQ_READ'
SCOPE int kseq_read(kseq_t *seq) \
^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c transcriptmapping.cpp -o transcriptmapping.o
transcriptmapping.cpp:605:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
sam_hdr_write(of, header);
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜
transcriptmapping.cpp:569:10: warning: unused function 'report_every_3_mins' [-Wunused-function]
void report_every_3_mins(atomic<unsigned long long> &cnt, atomic<bool> &running) {
^
In file included from transcriptmapping.cpp:2:
./transcriptmapping.h:138:15: warning: private field 'SOURCE' is not used [-Wunused-private-field]
const int SOURCE = 1;
^
./transcriptmapping.h:142:15: warning: private field 'SCORE' is not used [-Wunused-private-field]
const int SCORE = 5;
^
./transcriptmapping.h:144:15: warning: private field 'PHASE' is not used [-Wunused-private-field]
const int PHASE = 7;
^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp:92:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
sam_hdr_write(fp, hdr);
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o scPipe.so Gene.o Interval.o RcppExports.o cellbarcode.o detect_barcode.o parsebam.o parsecount.o rcpp_scPipe_func.o transcriptmapping.o trimbarcode.o utils.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/scPipe/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
* DONE (scPipe)
scPipe.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(scPipe)
Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
>
> test_check("scPipe")
[1] "organism/gene_id_type not provided. Make a guess: mmusculus_gene_ensembl / ensembl_gene_id"
══ testthat results ═══════════════════════════════════════════════════════════
OK: 14 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
10.118 0.516 10.717
scPipe.Rcheck/scPipe-Ex.timings
| name | user | system | elapsed | |
| QC_metrics | 0.830 | 0.010 | 0.846 | |
| UMI_dup_info | 0.156 | 0.009 | 0.165 | |
| UMI_duplication | 0.113 | 0.019 | 0.133 | |
| calculate_QC_metrics | 0.859 | 0.096 | 10.035 | |
| cell_barcode_matching | 0.105 | 0.004 | 0.109 | |
| convert_geneid | 0.398 | 0.016 | 3.867 | |
| create_processed_report | 0.002 | 0.000 | 0.002 | |
| create_report | 0.002 | 0.001 | 0.002 | |
| create_sce_by_dir | 0.103 | 0.003 | 0.107 | |
| demultiplex_info | 0.098 | 0.004 | 0.103 | |
| detect_outlier | 0.269 | 0.007 | 0.277 | |
| gene_id_type | 0.110 | 0.004 | 0.115 | |
| get_genes_by_GO | 0.256 | 0.019 | 3.175 | |
| organism | 0.129 | 0.005 | 0.134 | |
| plot_QC_pairs | 9.496 | 0.068 | 9.647 | |
| plot_UMI_dup | 0.306 | 0.007 | 0.325 | |
| plot_demultiplex | 0.371 | 0.005 | 0.381 | |
| plot_mapping | 0.877 | 0.016 | 0.922 | |
| remove_outliers | 0.309 | 0.005 | 0.316 | |
| sc_count_aligned_bam | 0.002 | 0.000 | 0.001 | |
| sc_demultiplex | 0.002 | 0.000 | 0.002 | |
| sc_demultiplex_and_count | 0.001 | 0.000 | 0.001 | |
| sc_detect_bc | 0.001 | 0.000 | 0.002 | |
| sc_exon_mapping | 0.003 | 0.001 | 0.003 | |
| sc_gene_counting | 0.003 | 0.000 | 0.004 | |
| sc_sample_data | 10.111 | 0.047 | 10.280 | |
| sc_sample_qc | 0.872 | 0.008 | 0.895 | |
| sc_trim_barcode | 0.002 | 0.000 | 0.003 | |