Closed JianGuoZhou3 closed 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
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
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
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...
However, I installed it on my MacBook. Thanks.