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 08:44:46 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scPipe.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings scPipe_1.2.1.tar.gz |
| StartedAt: 2018-10-17 04:42:38 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:48:32 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 354.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scPipe.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scPipe.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings scPipe_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/scPipe.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/scPipe/libs/i386/scPipe.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sc_sample_data 9.84 0.01 9.86
plot_QC_pairs 7.07 0.28 7.34
calculate_QC_metrics 1.44 0.01 8.33
convert_geneid 0.48 0.14 5.56
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_QC_pairs 8.53 0.07 8.61
sc_sample_data 7.49 0.02 7.50
calculate_QC_metrics 0.89 0.02 8.67
convert_geneid 0.52 0.00 5.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/scPipe.Rcheck/00check.log'
for details.
scPipe.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/scPipe_1.2.1.tar.gz && rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scPipe.buildbin-libdir scPipe_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL scPipe_1.2.1.zip && rm scPipe_1.2.1.tar.gz scPipe_1.2.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 1595k 100 1595k 0 0 21.7M 0 --:--:-- --:--:-- --:--:-- 23.9M
install for i386
* installing *source* package 'scPipe' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Gene.cpp -o Gene.o
Gene.cpp: In member function 'void Gene::flatten_exon()':
Gene.cpp:103:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 1; i < exon_vec.size(); i++)
^
Gene.cpp: In function 'std::ostream& operator<<(std::ostream&, const Gene&)':
Gene.cpp:128:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < obj.exon_vec.size(); ++i)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Interval.cpp -o Interval.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cellbarcode.cpp -o cellbarcode.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c detect_barcode.cpp -o detect_barcode.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c parsebam.cpp -o parsebam.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c parsecount.cpp -o parsecount.o
parsecount.cpp: In function 'void write_stat(std::string, std::string, std::vector<int>, std::unordered_map<std::basic_string<char>, UMI_dedup_stat>)':
parsecount.cpp:134:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<UMI_dup_count.size(); i++)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
In file included from rcpp_scPipe_func.cpp:7:0:
transcriptmapping.h: In member function 'void GeneBin::add_gene(Gene)':
transcriptmapping.h:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.st < start)
^
transcriptmapping.h:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.en > end)
^
transcriptmapping.h: In member function 'const bool GeneBin::overlaps(const Interval&)':
transcriptmapping.h:53:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.h:53:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
In file included from config_hts.h:8:0,
from trimbarcode.h:6,
from rcpp_scPipe_func.cpp:3:
trimbarcode.h: At global scope:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:170:16: warning: 'kseq_t* kseq_init(bioc_gzFile)' defined but not used [-Wunused-function]
SCOPE kseq_t *kseq_init(type_t fd) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
KSEQ_INIT(gzFile, gzread)
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:176:13: warning: 'void kseq_destroy(kseq_t*)' defined but not used [-Wunused-function]
SCOPE void kseq_destroy(kseq_t *ks) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
KSEQ_INIT(gzFile, gzread)
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:190:12: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
SCOPE int kseq_read(kseq_t *seq) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:242:2: note: in expansion of macro '__KSEQ_READ'
__KSEQ_READ(SCOPE)
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
KSEQ_INIT(gzFile, gzread)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c transcriptmapping.cpp -o transcriptmapping.o
In file included from transcriptmapping.cpp:2:0:
transcriptmapping.h: In member function 'void GeneBin::add_gene(Gene)':
transcriptmapping.h:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.st < start)
^
transcriptmapping.h:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.en > end)
^
transcriptmapping.h: In member function 'const bool GeneBin::overlaps(const Interval&)':
transcriptmapping.h:53:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.h:53:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.cpp: In member function 'int Mapping::map_exon(bam_hdr_t*, bam1_t*, std::string&, bool)':
transcriptmapping.cpp:464:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int c=0; c<b->core.n_cigar; c++)
^
transcriptmapping.cpp: In member function 'void Mapping::parse_align(std::string, std::string, bool, std::string, std::string, std::string, std::string, int, int)':
transcriptmapping.cpp:605:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(of, header);
^
transcriptmapping.cpp: At global scope:
transcriptmapping.cpp:569:10: warning: 'void {anonymous}::report_every_3_mins(std::atomic<long long unsigned int>&, std::atomic<bool>&)' defined but not used [-Wunused-function]
void report_every_3_mins(atomic<unsigned long long> &cnt, atomic<bool> &running) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp: In function 'void kseq_t_to_bam_t(kseq_t*, bam1_t*, int)':
trimbarcode.cpp:38:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->m_data < b->l_data)
^
trimbarcode.cpp: In function 'void paired_fastq_to_bam(char*, char*, char*, read_s, filter_s)':
trimbarcode.cpp:92:27: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'int hamming_distance(std::string, std::string)':
utils.cpp:14:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < A.length(); ++i)
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scPipe.dll tmp.def 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 -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/scPipe.buildbin-libdir/scPipe/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scPipe'
finding HTML links ... done
QC_metrics html
finding level-2 HTML links ... done
UMI_dup_info html
UMI_duplication html
calculate_QC_metrics html
cell_barcode_matching html
convert_geneid html
create_processed_report html
create_report html
create_sce_by_dir html
demultiplex_info html
detect_outlier html
gene_id_type html
get_genes_by_GO html
organism html
plot_QC_pairs html
plot_UMI_dup html
plot_demultiplex html
plot_mapping html
remove_outliers html
scPipe html
sc_count_aligned_bam html
sc_demultiplex html
sc_demultiplex_and_count html
sc_detect_bc html
sc_exon_mapping html
sc_gene_counting html
sc_sample_data html
sc_sample_qc html
sc_trim_barcode html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'scPipe' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Gene.cpp -o Gene.o
Gene.cpp: In member function 'void Gene::flatten_exon()':
Gene.cpp:103:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 1; i < exon_vec.size(); i++)
^
Gene.cpp: In function 'std::ostream& operator<<(std::ostream&, const Gene&)':
Gene.cpp:128:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < obj.exon_vec.size(); ++i)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Interval.cpp -o Interval.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cellbarcode.cpp -o cellbarcode.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c detect_barcode.cpp -o detect_barcode.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c parsebam.cpp -o parsebam.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c parsecount.cpp -o parsecount.o
parsecount.cpp: In function 'void write_stat(std::string, std::string, std::vector<int>, std::unordered_map<std::basic_string<char>, UMI_dedup_stat>)':
parsecount.cpp:134:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<UMI_dup_count.size(); i++)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
In file included from rcpp_scPipe_func.cpp:7:0:
transcriptmapping.h: In member function 'void GeneBin::add_gene(Gene)':
transcriptmapping.h:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.st < start)
^
transcriptmapping.h:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.en > end)
^
transcriptmapping.h: In member function 'const bool GeneBin::overlaps(const Interval&)':
transcriptmapping.h:53:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.h:53:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
In file included from config_hts.h:8:0,
from trimbarcode.h:6,
from rcpp_scPipe_func.cpp:3:
trimbarcode.h: At global scope:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:170:16: warning: 'kseq_t* kseq_init(bioc_gzFile)' defined but not used [-Wunused-function]
SCOPE kseq_t *kseq_init(type_t fd) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
KSEQ_INIT(gzFile, gzread)
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:176:13: warning: 'void kseq_destroy(kseq_t*)' defined but not used [-Wunused-function]
SCOPE void kseq_destroy(kseq_t *ks) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
KSEQ_INIT(gzFile, gzread)
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:190:12: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
SCOPE int kseq_read(kseq_t *seq) \
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:242:2: note: in expansion of macro '__KSEQ_READ'
__KSEQ_READ(SCOPE)
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
KSEQ_INIT(gzFile, gzread)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c transcriptmapping.cpp -o transcriptmapping.o
In file included from transcriptmapping.cpp:2:0:
transcriptmapping.h: In member function 'void GeneBin::add_gene(Gene)':
transcriptmapping.h:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.st < start)
^
transcriptmapping.h:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.en > end)
^
transcriptmapping.h: In member function 'const bool GeneBin::overlaps(const Interval&)':
transcriptmapping.h:53:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.h:53:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.cpp: In member function 'int Mapping::map_exon(bam_hdr_t*, bam1_t*, std::string&, bool)':
transcriptmapping.cpp:464:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int c=0; c<b->core.n_cigar; c++)
^
transcriptmapping.cpp: In member function 'void Mapping::parse_align(std::string, std::string, bool, std::string, std::string, std::string, std::string, int, int)':
transcriptmapping.cpp:605:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(of, header);
^
transcriptmapping.cpp: At global scope:
transcriptmapping.cpp:569:10: warning: 'void {anonymous}::report_every_3_mins(std::atomic<long long unsigned int>&, std::atomic<bool>&)' defined but not used [-Wunused-function]
void report_every_3_mins(atomic<unsigned long long> &cnt, atomic<bool> &running) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp: In function 'void kseq_t_to_bam_t(kseq_t*, bam1_t*, int)':
trimbarcode.cpp:38:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->m_data < b->l_data)
^
trimbarcode.cpp: In function 'void paired_fastq_to_bam(char*, char*, char*, read_s, filter_s)':
trimbarcode.cpp:92:27: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'int hamming_distance(std::string, std::string)':
utils.cpp:14:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < A.length(); ++i)
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scPipe.dll tmp.def 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 -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/scPipe.buildbin-libdir/scPipe/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scPipe' as scPipe_1.2.1.zip
* DONE (scPipe)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'scPipe' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
scPipe.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
9.17 0.82 10.00
|
scPipe.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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(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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
8.06 0.37 8.42
|
|
scPipe.Rcheck/examples_i386/scPipe-Ex.timings
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scPipe.Rcheck/examples_x64/scPipe-Ex.timings
|