安装R软件包时出错:使用Anaconda的scran

问题描述 投票:0回答:1

我正在使用anaconda下载名为scran的R包。尽管我已将其下载到我的R库路径,但收到错误消息。当我尝试在R环境中加载程序包时,它也失败了。我在macOS Catalina(10.15.4)上。我也尝试BiocManager::install(scran),但也失败了。

scran(https://bioconductor.org/packages/release/bioc/html/scran.html

有人可以帮我吗?非常感谢!请查看下面的详细信息。

#我使用conda install -c Bioconda bioconductor-scran下载了scran

(scrnaseq) yaochung41@x86_64-apple-darwin13 library % conda install -c bioconda bioconductor-scran
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/yaochung41/anaconda3/envs/scrnaseq

  added / updated specs:
    - bioconductor-scran


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2020.4.5.1 |       hecc5488_0         146 KB  conda-forge
    certifi-2020.4.5.1         |   py38h32f6830_0         151 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         297 KB

The following packages will be UPDATED:

  bioconductor-scran bioconda/label/cf201901::bioconductor~ --> bioconda::bioconductor-scran-1.14.1-r36h6de7cb9_0
  ca-certificates                     2019.11.28-hecc5488_0 --> 2020.4.5.1-hecc5488_0
  certifi                         2019.11.28-py38h32f6830_1 --> 2020.4.5.1-py38h32f6830_0


Proceed ([y]/n)? y


Downloading and Extracting Packages
ca-certificates-2020 | 146 KB    | ##################################### | 100% 
certifi-2020.4.5.1   | 151 KB    | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
INFO: deactivate-gfortran_osx-64.sh made the following environmental changes:
-DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/yaochung41/anaconda3/envs/scrnaseq/include -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
-DEBUG_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/yaochung41/anaconda3/envs/scrnaseq/include -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
-F77=/Users/yaochung41/anaconda3/envs/scrnaseq/bin/x86_64-apple-darwin13.4.0-gfortran
-F90=/Users/yaochung41/anaconda3/envs/scrnaseq/bin/x86_64-apple-darwin13.4.0-gfortran
-F95=/Users/yaochung41/anaconda3/envs/scrnaseq/bin/x86_64-apple-darwin13.4.0-gfortran
-FC=/Users/yaochung41/anaconda3/envs/scrnaseq/bin/x86_64-apple-darwin13.4.0-gfortran
-FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/yaochung41/anaconda3/envs/scrnaseq/include
-FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/yaochung41/anaconda3/envs/scrnaseq/include
-GFORTRAN=/Users/yaochung41/anaconda3/envs/scrnaseq/bin/x86_64-apple-darwin13.4.0-gfortran
(scrnaseq) yaochung41@x86_64-apple-darwin13 library % R

#然后尝试使用library(scran)从R 3.6.3加载程序包,并且我也收到错误

Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.

  Natural language support but running in an English locale

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(scran)
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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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
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, rowsum

Error: package or namespace load failed for ‘scran’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/yaochung41/anaconda3/envs/scrnaseq/lib/R/library/scran/libs/scran.dylib':
  dlopen(/Users/yaochung41/anaconda3/envs/scrnaseq/lib/R/library/scran/libs/scran.dylib, 6): Library not loaded: @rpath/libopenblasp-r0.3.7.dylib
  Referenced from: /Users/yaochung41/anaconda3/envs/scrnaseq/lib/R/library/scran/libs/scran.dylib
  Reason: image not found```


我正在使用anaconda下载名为scran的R软件包。尽管我已将其下载到我的R库路径,但收到错误消息。当我尝试在R环境中加载程序包时,它也失败了。我是...

r macos anaconda bioconductor
1个回答
0
投票

我遇到了您今天遇到的第二个错误,并且认为我已经找到了解决方法。

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