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Aufiero / circRNAprofiler

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Can't install #8

Closed JianGuoZhou3 closed 3 years ago

JianGuoZhou3 commented 3 years ago 
BiocManager::install("circRNAprofiler")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'circRNAprofiler'
also installing the dependencies ‘universalmotif’, ‘BSgenome.Hsapiens.UCSC.hg19’

trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/universalmotif_1.6.4.tar.gz'
Content type 'application/x-gzip' length 3723500 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz'
Content type 'application/x-gzip' length 710245413 bytes (677.3 MB)
==================================================
downloaded 677.3 MB

trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/circRNAprofiler_1.2.1.tar.gz'
Content type 'application/x-gzip' length 3769138 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

* installing *source* package ‘universalmotif’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG  -I'/home/zhou/Rlib/Rcpp/include' -I'/home/zhou/Rlib/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG  -I'/home/zhou/Rlib/Rcpp/include' -I'/home/zhou/Rlib/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -c add_multifreq.cpp -o add_multifreq.o
g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG  -I'/home/zhou/Rlib/Rcpp/include' -I'/home/zhou/Rlib/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -c compare_motifs.cpp -o compare_motifs.o
In file included from /home/zhou/Rlib/RcppThread/include/RcppThread.h:11:0,
                 from compare_motifs.cpp:2:
/home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp: In lambda function:
/home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp:42:19: error: parameter packs not expanded with ‘...’:
                 f(args...);
                   ^
/home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp:42:19: note:         ‘args’
/home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp:42:23: error: expansion pattern ‘args’ contains no argument packs
                 f(args...);
                       ^
In file included from /home/zhou/Rlib/RcppThread/include/RcppThread.h:13:0,
                 from compare_motifs.cpp:2:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In member function ‘void RcppThread::ThreadPool::push(F&&, Args&& ...)’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:31: error: expected ‘,’ before ‘...’ token
         jobs_.emplace([f, args...] { f(args...); });
                               ^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:31: error: expected identifier before ‘...’ token
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:34: error: parameter packs not expanded with ‘...’:
         jobs_.emplace([f, args...] { f(args...); });
                                  ^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:34: note:         ‘args’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In lambda function:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:44: error: expansion pattern ‘args’ contains no argument packs
         jobs_.emplace([f, args...] { f(args...); });
                                            ^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In member function ‘std::future<decltype (f(args ...))> RcppThread::ThreadPool::pushReturn(F&&, Args&& ...)’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:54: error: expected ‘,’ before ‘...’ token
     auto job = std::make_shared<jobPackage>([&f, args...] {
                                                      ^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:54: error: expected identifier before ‘...’ token
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:57: error: parameter packs not expanded with ‘...’:
     auto job = std::make_shared<jobPackage>([&f, args...] {
                                                         ^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:57: note:         ‘args’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In lambda function:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:147:22: error: expansion pattern ‘args’ contains no argument packs
         return f(args...);
                      ^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In instantiation of ‘struct RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]::__lambda5’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:9:   required from ‘void RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:201:9:   required from ‘void RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13&; ptrdiff_t = long int; size_t = long unsigned int]’
/home/zhou/Rlib/RcppThread/include/RcppThread/parallelFor.hpp:48:5:   required from ‘void RcppThread::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13; ptrdiff_t = long int; size_t = long unsigned int]’
compare_motifs.cpp:1426:18:   required from here
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:27: error: using invalid field ‘RcppThread::ThreadPool::push(F&&, Args&& ...)::__lambda5::__args’
         jobs_.emplace([f, args...] { f(args...); });
                           ^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In instantiation of ‘struct RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]::__lambda5’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:9:   required from ‘void RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:201:9:   required from ‘void RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14&; ptrdiff_t = long int; size_t = long unsigned int]’
/home/zhou/Rlib/RcppThread/include/RcppThread/parallelFor.hpp:48:5:   required from ‘void RcppThread::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14; ptrdiff_t = long int; size_t = long unsigned int]’
compare_motifs.cpp:1485:18:   required from here
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:27: error: using invalid field ‘RcppThread::ThreadPool::push(F&&, Args&& ...)::__lambda5::__args’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In instantiation of ‘struct RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]::__lambda5’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:9:   required from ‘void RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:201:9:   required from ‘void RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15&; ptrdiff_t = long int; size_t = long unsigned int]’
/home/zhou/Rlib/RcppThread/include/RcppThread/parallelFor.hpp:48:5:   required from ‘void RcppThread::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15; ptrdiff_t = long int; size_t = long unsigned int]’
compare_motifs.cpp:1859:18:   required from here
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:27: error: using invalid field ‘RcppThread::ThreadPool::push(F&&, Args&& ...)::__lambda5::__args’
make: *** [compare_motifs.o] Error 1
ERROR: compilation failed for package ‘universalmotif’
* removing ‘/home/zhou/Rlib/universalmotif’
* installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘BSgenome.Hsapiens.UCSC.hg19’:
 .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
  call: validObject(.Object)
  error: invalid class “TwoBitFile” object: undefined class for slot "resource" ("characterORconnection")
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/zhou/Rlib/BSgenome.Hsapiens.UCSC.hg19’
ERROR: dependencies ‘universalmotif’, ‘BSgenome.Hsapiens.UCSC.hg19’ are not available for package ‘circRNAprofiler’
* removing ‘/home/zhou/Rlib/circRNAprofiler’

The downloaded source packages are in
    ‘/tmp/RtmpiyGfYf/downloaded_packages’
Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign, KernSmooth,
  MASS, Matrix, mgcv, nlme, nnet, spatial, survival
Old packages: 'renv'
 BiocManager::valid("circRNAprofiler")
Error in file(con, "rb") : 
  cannot open the connection to 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES'
In addition: Warning message:
In file(con, "rb") :
  URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES': status was 'Timeout was reached'

sessionInfo() 
R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)  Matrix products: default BLAS:   /usr/local/lib64/R/lib/libRblas.so LAPACK: /usr/local/lib64/R/lib/libRlapack.so  locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8      [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                   [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C         attached base packages: [1] stats     graphics  grDevices utils     datasets  methods   base       loaded via a namespace (and not attached): [1] edgeR_3.32.0        BiocManager_1.30.10 compiler_4.0.2      limma_3.46.0        tools_4.0.2         [6] Rcpp_1.0.6          grid_4.0.2          locfit_1.5-9.4      lattice_0.20-41
--
 
JianGuoZhou3 commented 3 years ago

@Aufiero please help me to check this error. And in my Macbook also have another error.

BiocManager::install("circRNAprofiler")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.3
  (2020-10-10)
Installing package(s) 'circRNAprofiler'
also installing the dependency ‘BSgenome.Hsapiens.UCSC.hg19’

trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/circRNAprofiler_1.2.1.tgz'
Content type 'application/x-gzip' length 3449297 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

The downloaded binary packages are in
    /var/folders/h1/wph5l7kn6sq020007z1bq2d00000gn/T//RtmpBIE2Nh/downloaded_packages
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz'
Content type 'application/x-gzip' length 710245413 bytes (677.3 MB)
======================================
downloaded 523.5 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 548952376 != reported length 710245413
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘BSgenome.Hsapiens.UCSC.hg19’ failed
Old packages: 'rstpm2', 'Hmisc', 'ipred', 'isoband',
  'MatrixModels', 'tidyBF', 'tidyr', 'tinytex'
Update all/some/none? [a/s/n]:

I tried used package archive file install.

 install.packages("/Volumes/ZJG/downloads/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz", repos = NULL, 
+                                      type = "source", lib="/Library/Frameworks/R.framework/Versions/4.0/Resources/library")
Warning: invalid package ‘/Volumes/ZJG/downloads/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz’
Error: ERROR: no packages specified
Warning in install.packages :
  installation of package ‘/Volumes/ZJG/downloads/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz’ had non-zero exit status
> install.packages("/Users/jianguozhou/Downloads/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz", repos = NULL, 
+                                      type = "source", lib="/Library/Frameworks/R.framework/Versions/4.0/Resources/library")
* installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL") 
2: undefined slot classes in definition of "XInteger": elementMetadata(class "DataTable_OR_NULL") 
3: undefined slot classes in definition of "XDouble": elementMetadata(class "DataTable_OR_NULL") 
4: multiple methods tables found for ‘which’ 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL")
Warning: undefined slot classes in definition of "XInteger": elementMetadata(class "DataTable_OR_NULL")
Warning: undefined slot classes in definition of "XDouble": elementMetadata(class "DataTable_OR_NULL")
Warning: multiple methods tables found for ‘which’
Error: package or namespace load failed for ‘BSgenome.Hsapiens.UCSC.hg19’:
 .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
  call: validObject(.Object)
  error: invalid class “TwoBitFile” object: undefined class for slot "resource" ("characterORconnection")
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BSgenome.Hsapiens.UCSC.hg19’
Warning in install.packages :
  installation of package ‘/Users/jianguozhou/Downloads/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz’ had non-zero exit status
>

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS High Sierra 10.13.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets [6] methods base
loaded via a namespace (and not attached): [1] XVector_0.30.0
[2] GenomeInfoDb_1.26.2
[3] pillar_1.5.0
[4] compiler_4.0.3
[5] BiocManager_1.30.10
[6] formatR_1.7
[7] futile.logger_1.4.3
[8] MatrixGenerics_1.2.1
[9] zlibbioc_1.36.0
[10] bitops_1.0-6
[11] futile.options_1.0.1
[12] tools_4.0.3
[13] lattice_0.20-41
[14] lifecycle_1.0.0
[15] tibble_3.1.0
[16] gtable_0.3.0
[17] BSgenome_1.56.0
[18] pkgconfig_2.0.3
[19] rlang_0.4.10
[20] Matrix_1.3-2
[21] DelayedArray_0.16.1
[22] rstudioapi_0.13
[23] DBI_1.1.1
[24] parallel_4.0.3
[25] VennDiagram_1.6.20
[26] xfun_0.21
[27] GenomeInfoDbData_1.2.4
[28] gridExtra_2.3
[29] rtracklayer_1.48.0
[30] dplyr_1.0.4
[31] knitr_1.31
[32] Biostrings_2.56.0
[33] generics_0.1.0
[34] vctrs_0.3.6
[35] S4Vectors_0.28.1
[36] IRanges_2.24.1
[37] stats4_4.0.3
[38] grid_4.0.3
[39] tidyselect_1.1.0
[40] Biobase_2.50.0
[41] glue_1.4.2
[42] R6_2.5.0
[43] fansi_0.4.2
[44] XML_4.0-0
[45] BiocParallel_1.24.1
[46] purrr_0.3.4
[47] lambda.r_1.2.4
[48] magrittr_2.0.1
[49] GenomicAlignments_1.24.0
[50] Rsamtools_2.4.0
[51] GenomicRanges_1.42.0
[52] ellipsis_0.3.1
[53] matrixStats_0.58.0
[54] BiocGenerics_0.36.0
[55] SummarizedExperiment_1.20.0 [56] assertthat_0.2.1
[57] utf8_1.1.4
[58] RCurl_1.98-1.2
[59] crayon_1.4.1

Aufiero commented 3 years ago

Hi,

I see that you have the Bioconductor version: Release (3.11), you should have the Bioconductor version: Release (3.12).

To update Bioconductor run: BiocManager::install(version = "3.12")

Then try to install the release version of circRNAprofiler in Bioconductor 3.12 with. BiocManager::install("circRNAprofiler")

Please wait until Monday to reinstall circRNAprofiler, so that you can take the latest changes that I committed.

Let me know if this solves the problem.

Best, S

JianGuoZhou3 commented 3 years ago

Hi,

I see that you have the Bioconductor version: Release (3.11), you should have the Bioconductor version: Release (3.12).

To update Bioconductor run: BiocManager::install(version = "3.12")

Then try to install the release version of circRNAprofiler in Bioconductor 3.12 with. BiocManager::install("circRNAprofiler")

Please wait until Monday to reinstall circRNAprofiler, so that you can take the latest changes that I committed.

Let me know if this solves the problem.

Best, S

Thanks for your update, best. Jian-Guo

JianGuoZhou3 commented 3 years ago 
BiocManager::install(version = "3.12")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installation path not writeable, unable to update packages: boot,
  class, cluster, codetools, foreign, KernSmooth, MASS, Matrix, mgcv,
  nlme, nnet, spatial, survival
Old packages: 'renv'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://mirrors.sjtug.sjtu.edu.cn/cran/src/contrib/renv_0.13.0.tar.gz'
Content type 'application/gzip' length 413734 bytes (404 KB)
==================================================
downloaded 404 KB

* installing *source* package ‘renv’ ...
** package ‘renv’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘renv’:
 .onLoad failed in loadNamespace() for 'renv', details:
  call: if (last %in% endings) return(TRUE)
  error: argument is of length zero
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/zhou/Rlib/renv’
* restoring previous ‘/home/zhou/Rlib/renv’

The downloaded source packages are in
    ‘/tmp/RtmpL785UM/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘renv’ had non-zero exit status

Hi @Aufiero still didn't work... Please check this...

JianGuoZhou3 commented 3 years ago

However, I installed it on my MacBook. Thanks.