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1051444231 • 0
@38322dcf
Last seen 4 weeks ago
China

library(AnnotationDbi) 载入需要的程辑包:stats4 载入需要的程辑包:BiocGenerics

载入程辑包:‘BiocGenerics’

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame,
basename, cbind, colnames, dirname,
do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, Map,
mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce,
rownames, sapply, setdiff, sort,
table, tapply, union, unique,
unsplit, which.max, which.min

载入需要的程辑包:Biobase Welcome to Bioconductor

Vignettes contain introductory
material; view with
'browseVignettes()'. To cite
Bioconductor, see
'citation("Biobase")', and for
packages 'citation("pkgname")'.

载入需要的程辑包:IRanges 载入需要的程辑包:S4Vectors

载入程辑包:‘S4Vectors’

The following objects are masked from ‘package:base’:

expand.grid, I, unname

载入程辑包:‘IRanges’

The following object is masked from ‘package:grDevices’:

windows

library(AnnotationDbi) BiocManager::install('org.Hs.eg.db') #下载相应的包 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22 ucrt) Installing package(s) 'org.Hs.eg.db' 安装源码包‘org.Hs.eg.db’

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/org.Hs.eg.db_3.15.0.tar.gz' Content type 'application/x-gzip' length 83788492 bytes (79.9 MB) downloaded 79.9 MB

  • installing source package 'org.Hs.eg.db' ... using staged installation R inst byte-compile and prepare package for lazy loading Error: package 'AnnotationDbi' required by 'org.Hs.eg.db' could not be found Execution halted ERROR: lazy loading failed for package 'org.Hs.eg.db'
  • removing 'C:/Users/H/AppData/Local/R/win-library/4.2/org.Hs.eg.db'
TargetScoreData • 253 views
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Guido Hooiveld ★ 3.3k
@guido-hooiveld-2020
Last seen 8 hours ago
Wageningen University, Wageningen, the …
Error: package 'AnnotationDbi' required by 'org.Hs.eg.db' could not be found. Execution halted.

Means, ehh, that the required package AnnotationDbi is not yet installed on your system.

Thus, restart R en do:

BiocManager::install("AnnotationDbi")
BiocManager::install("org.Hs.eg.db")

It can also be helpfull to have Rtools installed: https://cran.r-project.org/bin/windows/Rtools/rtools42/rtools.html (links to Rtools for R-4.2.x)

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BiocManager::install("AnnotationDbi",force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.3 (2022-03-10) Installing package(s) 'AnnotationDbi' trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/AnnotationDbi_1.56.2.zip' Content type 'application/zip' length 5387247 bytes (5.1 MB) downloaded 5.1 MB

package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\H\AppData\Local\Temp\Rtmpc373KX\downloaded_packages Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.1.3/library packages: cluster, MASS, Matrix, mgcv, nlme, survival Old packages: 'openssl' Update all/some/none? [a/s/n]: n

BiocManager::install("org.Hs.eg.db") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.3 (2022-03-10) Installing package(s) 'org.Hs.eg.db' 安装源码包‘org.Hs.eg.db’

trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Hs.eg.db_3.14.0.tar.gz' Content type 'application/x-gzip' length 82195112 bytes (78.4 MB) downloaded 78.4 MB

  • installing source package 'org.Hs.eg.db' ... using staged installation R inst byte-compile and prepare package for lazy loading 错误: 找不到'org.Hs.eg.db'所需要的程辑包'AnnotationDbi' 停止执行 ERROR: lazy loading failed for package 'org.Hs.eg.db'
  • removing 'C:/Users/H/Documents/R/win-library/4.1/org.Hs.eg.db'

It dosen't work

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 Installation paths not writeable, unable to update packages
  • Now you are using R-4.1, but your first post is on the use of R-4.2!
  • Anyway, start R with sufficient rights (thus as local admin).
  • It is always useful to have Rtools installed. Be sure to use the proper version that matches your version of R. https://cran.r-project.org/bin/windows/Rtools/
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I have updated Rtools

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BiocManager::install("AnnotationDbi",force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22 ucrt) Installing package(s) 'AnnotationDbi' trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/windows/contrib/4.2/AnnotationDbi_1.58.0.zip' Content type 'application/zip' length 5242384 bytes (5.0 MB) downloaded 5.0 MB

程序包‘AnnotationDbi’打开成功,MD5和检查也通过

下载的二进制程序包在 C:\Users\H\AppData\Local\Temp\RtmpKCd3lm\downloaded_packages里 Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.2.0/library packages: MASS Old packages: 'openssl' Update all/some/none? [a/s/n]: n

library(AnnotationDbi) 载入需要的程辑包:stats4 载入需要的程辑包:IRanges 载入需要的程辑包:S4Vectors

载入程辑包:‘S4Vectors’

The following objects are masked from ‘package:dplyr’:

first, rename

The following objects are masked from ‘package:base’:

expand.grid, I, unname

载入程辑包:‘IRanges’

The following objects are masked from ‘package:dplyr’:

collapse, desc, slice

The following object is masked from ‘package:grDevices’:

windows

载入程辑包:‘AnnotationDbi’

The following object is masked from ‘package:dplyr’:

select

BiocManager::install("org.Hs.eg.db") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22 ucrt) Installing package(s) 'org.Hs.eg.db' 安装源码包‘org.Hs.eg.db’

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/org.Hs.eg.db_3.15.0.tar.gz' Content type 'application/x-gzip' length 83788492 bytes (79.9 MB) downloaded 79.9 MB

  • installing source package 'org.Hs.eg.db' ... using staged installation R inst byte-compile and prepare package for lazy loading Error: package 'AnnotationDbi' required by 'org.Hs.eg.db' could not be found Execution halted ERROR: lazy loading failed for package 'org.Hs.eg.db'
  • removing 'C:/Users/H/AppData/Local/R/win-library/4.2/org.Hs.eg.db'
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what is the result of .libPaths() and "AnnotationDbi" %in% rownames(installed.packages())

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