Entering edit mode
> if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
Installing package into ‘C:/Users/1021/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/BiocManager_1.30.19.zip'
Content type 'application/zip' length 336601 bytes (328 KB)
downloaded 328 KB
package ‘BiocManager’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\1021\AppData\Local\Temp\RtmpExczHU\downloaded_packages
> BiocManager::install("org.Hs.eg.db")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://mirror.lzu.edu.cn/CRAN
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
Installing package(s) 'BiocVersion', 'org.Hs.eg.db'
also installing the dependencies ‘sys’, ‘bitops’, ‘cli’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘askpass’, ‘zlibbioc’, ‘RCurl’, ‘GenomeInfoDbData’, ‘bit’, ‘rlang’, ‘vctrs’, ‘cachem’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘XVector’, ‘GenomeInfoDb’, ‘crayon’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘Rcpp’, ‘plogr’, ‘httr’, ‘png’, ‘Biostrings’, ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘DBI’, ‘RSQLite’, ‘S4Vectors’, ‘KEGGREST’, ‘AnnotationDbi’
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/sys_3.4.1.zip'
Content type 'application/zip' length 46654 bytes (45 KB)
downloaded 45 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/bitops_1.0-7.zip'
Content type 'application/zip' length 31679 bytes (30 KB)
downloaded 30 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/cli_3.6.0.zip'
Content type 'application/zip' length 1297492 bytes (1.2 MB)
downloaded 1.2 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/glue_1.6.2.zip'
Content type 'application/zip' length 162306 bytes (158 KB)
downloaded 158 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/lifecycle_1.0.3.zip'
Content type 'application/zip' length 138954 bytes (135 KB)
downloaded 135 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/fastmap_1.1.0.zip'
Content type 'application/zip' length 126556 bytes (123 KB)
downloaded 123 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/askpass_1.1.zip'
Content type 'application/zip' length 72278 bytes (70 KB)
downloaded 70 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/zlibbioc_1.44.0.zip'
Content type 'application/zip' length 206829 bytes (201 KB)
downloaded 201 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/RCurl_1.98-1.10.zip'
Content type 'application/zip' length 4286813 bytes (4.1 MB)
downloaded 4.1 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/bit_4.0.5.zip'
Content type 'application/zip' length 1131247 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/rlang_1.0.6.zip'
Content type 'application/zip' length 1576414 bytes (1.5 MB)
downloaded 1.5 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/vctrs_0.5.2.zip'
Content type 'application/zip' length 1376717 bytes (1.3 MB)
downloaded 1.3 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/cachem_1.0.6.zip'
Content type 'application/zip' length 71192 bytes (69 KB)
downloaded 69 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/curl_5.0.0.zip'
Content type 'application/zip' length 2621994 bytes (2.5 MB)
downloaded 2.5 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/jsonlite_1.8.4.zip'
Content type 'application/zip' length 1105104 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/mime_0.12.zip'
Content type 'application/zip' length 40621 bytes (39 KB)
downloaded 39 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/openssl_2.0.5.zip'
Content type 'application/zip' length 2651133 bytes (2.5 MB)
downloaded 2.5 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/R6_2.5.1.zip'
Content type 'application/zip' length 84197 bytes (82 KB)
downloaded 82 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/XVector_0.38.0.zip'
Content type 'application/zip' length 617092 bytes (602 KB)
downloaded 602 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/GenomeInfoDb_1.34.9.zip'
Content type 'application/zip' length 4169904 bytes (4.0 MB)
downloaded 847 KB
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/GenomeInfoDb_1.34.9.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 867878 != reported length 4169904
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/GenomeInfoDb_1.34.9.zip': Timeout of 300 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘GenomeInfoDb’ failed
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/crayon_1.5.2.zip'
Content type 'application/zip' length 162755 bytes (158 KB)
downloaded 158 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/bit64_4.0.5.zip'
Content type 'application/zip' length 493040 bytes (481 KB)
downloaded 481 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/blob_1.2.3.zip'
Content type 'application/zip' length 48443 bytes (47 KB)
downloaded 47 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/memoise_2.0.1.zip'
Content type 'application/zip' length 50175 bytes (48 KB)
downloaded 48 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/pkgconfig_2.0.3.zip'
Content type 'application/zip' length 22515 bytes (21 KB)
downloaded 21 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/Rcpp_1.0.10.zip'
Content type 'application/zip' length 2819280 bytes (2.7 MB)
downloaded 2.7 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/plogr_0.2.0.zip'
Content type 'application/zip' length 19035 bytes (18 KB)
downloaded 18 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/httr_1.4.4.zip'
Content type 'application/zip' length 518776 bytes (506 KB)
downloaded 506 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/png_0.1-8.zip'
Content type 'application/zip' length 190849 bytes (186 KB)
downloaded 186 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/Biostrings_2.66.0.zip'
Content type 'application/zip' length 13895265 bytes (13.3 MB)
downloaded 2.1 MB
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/Biostrings_2.66.0.zip' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 2178597 != reported length 13895265
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/Biostrings_2.66.0.zip': Timeout of 300 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘Biostrings’ failed
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/BiocGenerics_0.44.0.zip'
Content type 'application/zip' length 613075 bytes (598 KB)
downloaded 598 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/Biobase_2.58.0.zip'
Content type 'application/zip' length 2443861 bytes (2.3 MB)
downloaded 2.3 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/IRanges_2.32.0.zip'
Content type 'application/zip' length 2281420 bytes (2.2 MB)
downloaded 2.2 MB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/DBI_1.1.3.zip'
Content type 'application/zip' length 767134 bytes (749 KB)
downloaded 749 KB
trying URL 'https://mirror.lzu.edu.cn/CRAN/bin/windows/contrib/4.2/RSQLite_2.2.20.zip'
Content type 'application/zip' length 1536502 bytes (1.5 MB)
downloaded 1.5 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/S4Vectors_0.36.1.zip'
Content type 'application/zip' length 2078678 bytes (2.0 MB)
downloaded 2.0 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/KEGGREST_1.38.0.zip'
Content type 'application/zip' length 178785 bytes (174 KB)
downloaded 174 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/AnnotationDbi_1.60.0.zip'
Content type 'application/zip' length 5244154 bytes (5.0 MB)
downloaded 5.0 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/BiocVersion_3.16.0.zip'
Content type 'application/zip' length 8274 bytes
downloaded 8274 bytes
package ‘sys’ successfully unpacked and MD5 sums checked
package ‘bitops’ successfully unpacked and MD5 sums checked
package ‘cli’ successfully unpacked and MD5 sums checked
package ‘glue’ successfully unpacked and MD5 sums checked
package ‘lifecycle’ successfully unpacked and MD5 sums checked
package ‘fastmap’ successfully unpacked and MD5 sums checked
package ‘askpass’ successfully unpacked and MD5 sums checked
package ‘zlibbioc’ successfully unpacked and MD5 sums checked
package ‘RCurl’ successfully unpacked and MD5 sums checked
package ‘bit’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
package ‘vctrs’ successfully unpacked and MD5 sums checked
package ‘cachem’ successfully unpacked and MD5 sums checked
package ‘curl’ successfully unpacked and MD5 sums checked
package ‘jsonlite’ successfully unpacked and MD5 sums checked
package ‘mime’ successfully unpacked and MD5 sums checked
package ‘openssl’ successfully unpacked and MD5 sums checked
package ‘R6’ successfully unpacked and MD5 sums checked
package ‘XVector’ successfully unpacked and MD5 sums checked
package ‘crayon’ successfully unpacked and MD5 sums checked
package ‘bit64’ successfully unpacked and MD5 sums checked
package ‘blob’ successfully unpacked and MD5 sums checked
package ‘memoise’ successfully unpacked and MD5 sums checked
package ‘pkgconfig’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘plogr’ successfully unpacked and MD5 sums checked
package ‘httr’ successfully unpacked and MD5 sums checked
package ‘png’ successfully unpacked and MD5 sums checked
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘IRanges’ successfully unpacked and MD5 sums checked
package ‘DBI’ successfully unpacked and MD5 sums checked
package ‘RSQLite’ successfully unpacked and MD5 sums checked
package ‘S4Vectors’ successfully unpacked and MD5 sums checked
package ‘KEGGREST’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked
package ‘BiocVersion’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\1021\AppData\Local\Temp\RtmpExczHU\downloaded_packages
installing the source packages ‘GenomeInfoDbData’, ‘org.Hs.eg.db’
trying URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz'
Content type 'application/x-gzip' length 11725198 bytes (11.2 MB)
downloaded 5.2 MB
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 5481332 != reported length 11725198
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz': Timeout of 300 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘GenomeInfoDbData’ failed
trying URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz'
Content type 'application/x-gzip' length 88437137 bytes (84.3 MB)
downloaded 4.9 MB
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 5094504 != reported length 88437137
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz': Timeout of 300 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘org.Hs.eg.db’ failed
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.2/library
packages:
boot, class, codetools, foreign, MASS, Matrix, nlme, spatial, survival
> library("org.Hs.eg.db")
Error in library("org.Hs.eg.db") :
there is no package called ‘org.Hs.eg.db’
>
or
> options(connectionObserver = NULL)
> if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
> BiocManager::install("org.Hs.eg.db")
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
Installing package(s) 'org.Hs.eg.db'
安装源码包‘org.Hs.eg.db’
试开URL’https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz'
Content type 'application/x-gzip' length 88437137 bytes (84.3 MB)
downloaded 5.1 MB
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz' failed
此外: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 5334584 != reported length 88437137
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz': Timeout of 300 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
下载程序包‘org.Hs.eg.db’时出了问题
It looks like there is a timeout of 300 seconds. Could you try increasing the timeout
options(timeout=1000000)to see if that helps.