我的电脑内部有一千多个生物信息学多组学数据处理关联的r包,最近三五年基本上莫得何如安设过新的包,然则最近在一个新电脑内部进行视频号直播的时候发现底下的代码读取cel文献神色的affymetrix抒发量芯片的时候其实是会自动安设一个包:
library(oligo) celFiles <- list.celfiles('../cel_files/',listGzipped = T, full.name=TRUE) exon_data <- oligo::read.celfiles( celFiles )
如下所示:
> celFiles [1] "../cel_files//GSM756992_KS1-HG_U133A_2-2757.CEL.gz" [2] "../cel_files//GSM756993_KS1-HG_U133A_2-2871.CEL.gz" [3] "../cel_files//GSM756994_KS1-HG_U133A_2-2901.CEL.gz" [4] "../cel_files//GSM756995_KS1-HG_U133A_2-2905.CEL.gz" Loading required package: pd.hg.u133a.2Attempting to obtain 'pd.hg.u133a.2' from BioConductor website.Checking to see if your internet connection works...'getOption("repos")' replaces Bioconductor standard repositories, see'help("repositories", package = "BiocManager")' for details.Replacement repositories: CRAN: https://cran.rstudio.com/
假如你不使用bioconductor的镜像然则你又在中国大陆地区,就会遭受底下的报错;
遗漏分析:上期奖号遗漏总值为48,比前期遗漏总值低了2点,开出14个热码奖号,比前期热码多出现2个,开出4个温码奖号,比前期温码少出现1个,开出2个冷码奖号,比前期冷码少出现1个,最近10期奖号冷温热码个数比为21:59:120,遗漏总值出现范围在41-69之间,本期预计冷温热码个数比为1:3:16,看好遗漏总值出现在30附近。
福彩快乐8第2024174期(上周二)开奖回顾:03 05 16 19 20 24 35 36 40 44 46 53 54 58 62 64 66 69 75 80,其中奖号四区比为5:4:5:6,冷温热码比为3:4:13。
试开URL’https://bioconductor.org/packages/3.17/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz'Content type 'application/gzip' length 9843108 bytes (9.4 MB)downloaded 6.3 MBError in download.file(url, destfile, method, mode = "wb", ...) : download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz' failed此外: Warning messages:1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 0 != reported length 02: In download.file(url, destfile, method, mode = "wb", ...) : URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.17/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz': status was 'Transferred a partial file'Warning in download.packages(pkgs, destdir = tmpd, available = available, : 下载神色包'pd.hg.u133a.2’时出了问题载入需要的程辑包:pd.hg.u133a.2There was a problem during download or installation.Package 'pd.hg.u133a.2' cannot be loaded. Please, try again.Error in oligo::read.celfiles(celFiles) : The annotation package, pd.hg.u133a.2, could not be loaded.此外: Warning message:In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : 不存在叫'pd.hg.u133a.2’这个名字的程辑包
在中国大陆,其实网罗问题很是恶心的,下载一个 (9.4 MB)的包需要三五年的本领,何况大约率会失败,比如我上头就只是是下载了 6.3 MB 是一个不完好的包,是以安设会失败。这个时候需要确立一下本领问题:
getOption('timeout')options(timeout=10000)
就算是这么,群众也不成能说去恭候三五年去安设一个r包,是以就需要镜像匡助你。假如你使用了传统的镜像地址,等于咱们一直推选的清华大学的镜像:
小程序开发rm(list = ls()) options()$repos options()$BioC_mirror#options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))options()$repos options()$BioC_mirror
会发现,仍然是会报错,如下所示:
载入需要的程辑包:pd.hg.u133a.2Attempting to obtain 'pd.hg.u133a.2' from BioConductor website.Checking to see if your internet connection works...'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",package = "BiocManager")' for details.Replacement repositories: CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/Warning: 无法在貯藏處http://mirrors.tuna.tsinghua.edu.cn/bioconductor//packages/3.17/bioc/src/contrib中读写索引: 无法灵通URL'http://mirrors.tuna.tsinghua.edu.cn/bioconductor//packages/3.17/bioc/src/contrib/PACKAGES'Warning: 无法在貯藏處http://mirrors.tuna.tsinghua.edu.cn/bioconductor//packages/3.17/data/annotation/src/contrib中读写索引: 无法灵通URL'http://mirrors.tuna.tsinghua.edu.cn/bioconductor//packages/3.17/data/annotation/src/contrib/PACKAGES'Warning: 无法在貯藏處http://mirrors.tuna.tsinghua.edu.cn/bioconductor//packages/3.17/data/experiment/src/contrib中读写索引: 无法灵通URL'http://mirrors.tuna.tsinghua.edu.cn/bioconductor//packages/3.17/data/experiment/src/contrib/PACKAGES'Warning: 无法在貯藏處http://mirrors.tuna.tsinghua.edu.cn/bioconductor//packages/3.17/workflows/src/contrib中读写索引: 无法灵通URL'http://mirrors.tuna.tsinghua.edu.cn/bioconductor//packages/3.17/workflows/src/contrib/PACKAGES'Package 'pd.hg.u133a.2' was not found in the BioConductor repository.The 'pdInfoBuilder' package can often be used in situations like this.Error in oligo::read.celfiles(celFiles) : The annotation package, pd.hg.u133a.2, could not be loaded.
要是群众灵通上头的URL就会发现是;404 Not Found nginx/1.22.1 ,因为清华大学咫尺启动量入为用资源了,物联网app开发别说是3.17了,哪怕是3.18皆不是主要的凯旋下载,咫尺(2024年05月26日 )能凯旋下载的 是 3.19,何况需要合营4.4版块的r,而我的电脑照旧4.3,是以就很过问。咱们的马拉松助教团队给群众整理了这个问题:
凭证 Bioconductor 的安排,在 5 月 15 日,3.18 及此前版块的关联数据还是被存档,并从其同步开始中被移除。为量入为用镜像站磁盘空间,清华源等也相应移除了这些文献。要是群众咫尺使用的R言语是 4.3 ,Bioconductor 版块是 3.18 ,那么使用 BiocManager::install 的时候可能会报错 Warning: unable to access index for repository *** ,cannot open URL ***
咱们检讨一下 :https://new.bioconductor.org/about/mirrors/ 官方网站,发现bioconductor有新的镜像经受啦,如下所示真的立:
options(BioC_mirror="https://mirrors.westlake.edu.cn/bioconductor")
不错看到就奏效了:
试开URL’https://mirrors.westlake.edu.cn/bioconductor/packages/3.17/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz'Content type 'application/gzip' length 9843108 bytes (9.4 MB)downloaded 9.4 MB* installing *source* package 'pd.hg.u133a.2' ...** using staged installation** R** data** 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** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (pd.hg.u133a.2)下载的神色包在 'C:\Users\jimmy\AppData\Local\Temp\RtmpS0j9qK\downloaded_packages’里载入需要的程辑包:pd.hg.u133a.2载入需要的程辑包:RSQLite载入需要的程辑包:DBIPlatform design info loaded.
然则这个并不是一劳久逸的惩处决策,因为西湖大学也有可能会把 bioconductor的 3.18以 及此前版块的关联bioconductor包文献数据存档,并从其同步开始中被移除,为量入为用镜像站磁盘空间。
另外一个惩处决策,等于手动找到每个包的具体地址,使用底下的代码 :
install.packages("https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz",type = 'source',repos = NULL)
不错看到清华大学内部的包照旧许多:https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/release/data/annotation/src/contrib/ ,每个具体的包皆不错右键复制粘贴它们的真实下载地址哦:
图片
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