安装一个不存在的R包

也就是说，这个包是被删除了，在 https://bioconductor.org/about/removed-packages/ 
可以看到是很早之前，就被删除了。
如何安装被移除的R包呢
这个其实跟我之前讲解的如何安装旧版R包有异曲同工之妙。

留给读者解决吧，相信你粉了我们生信技能树这么久，这一点实力，还是可以有的！

# 解压
tar -xf IlluminaHumanMethylation450k.db_2.0.7.tar.gz

# 'BiocGenerics','S4Vectors','IRanges', 'Biobase', 'BiocGenerics', 'AnnotationDbi', 'org.Hs.eg.db', 'AnnotationForge'
# "bit", "plogr", "blob", "bit64", 'S4Vectors', 'RSQLite', 'DBI','RSQLite','remotes'

AnnotationForge:::createSimpleBimap 
替换为下边的代码，因为报错找不到 createSimpleBimap；发现包换了
AnnotationDbi::createSimpleBimap

library(remotes)
remotes::install_local("IlluminaHumanMethylation450k.db")

Warning message:
'IlluminaHumanMethylation450k.db' is deprecated.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Deprecated")

# could not find function "dbGetQuery"
library(DBI)
library(IlluminaHumanMethylation450k.db)
IlluminaHumanMethylation450k.db::IlluminaHumanMethylation450k()

# IlluminaHumanMethylation450kACCNUM has 365088 mapped keys (of 365088 keys)
# IlluminaHumanMethylation450kALIAS2PROBE has 74043 mapped keys (of 143558 keys)
# IlluminaHumanMethylation450kCHR has 331568 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kCHRLENGTHS has 93 mapped keys (of 640 keys)
# IlluminaHumanMethylation450kCHRLOC has 331443 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kCHRLOCEND has 331443 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kENSEMBL has 319028 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kENSEMBL2PROBE has 18604 mapped keys (of 39708 keys)
# IlluminaHumanMethylation450kENTREZID has 331594 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kENZYME has 38658 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kENZYME2PROBE has 925 mapped keys (of 975 keys)
# IlluminaHumanMethylation450kGENENAME has 331594 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kGO has 302014 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kGO2ALLPROBES has 13290 mapped keys (of 22963 keys)
# IlluminaHumanMethylation450kGO2PROBE has 10083 mapped keys (of 18933 keys)
# IlluminaHumanMethylation450kMAP has 330724 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kOMIM has 240300 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kPATH has 97051 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kPATH2PROBE has 214 mapped keys (of 229 keys)
# IlluminaHumanMethylation450kPMID has 330468 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kPMID2PROBE has 275464 mapped keys (of 754859 keys)
# IlluminaHumanMethylation450kREFSEQ has 331594 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kSYMBOL has 331594 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kUNIPROT has 316916 mapped keys (of 482931 keys)

# 探针与基因名的对应关系
IlluminaHumanMethylation450kSYMBOL
# 染色体信息
IlluminaHumanMethylation450kMAP
IlluminaHumanMethylation450kCHRLOC
IlluminaHumanMethylation450kCHRLOCEND
IlluminaHumanMethylation450kCHRLENGTHS

a=IlluminaHumanMethylation450k.db::IlluminaHumanMethylation450kSYMBOL
b=as.data.frame(a)
head(b)
#     probe_id symbol
# 1 cg03123289   A1BG
# 2 cg03630821   A1BG
# 3 cg10734734   A1BG
# 4 cg11001216   A1BG
# 5 cg14222245   A1BG
# 6 cg22286978   A1BG

BiocManager::install("FDb.InfiniumMethylation.hg19")
library(FDb.InfiniumMethylation.hg19)
FDb.InfiniumMethylation.hg19::FDb.InfiniumMethylation.hg19
# FeatureDb object:
# | Db type: FeatureDb
# | Supporting package: GenomicFeatures
# | data_nrow: 487173
# | Db created by: GenomicFeatures package from Bioconductor
# | Creation time: 2013-05-07 17:02:12 -0700 (Tue, 07 May 2013)
# | GenomicFeatures version at creation time: 1.13.2
# | RSQLite version at creation time: 0.11.3
# | DBSCHEMAVERSION: 1.0
# | Data source: NCBI/GEO and dbSNP
# | Genome: hg19
# | Resource: Illumina Infinium DNA methylation probes, mapped to hg19
# | Genus and Species: Homo sapiens
# | URL: ftp://ftp.illumina.com

hm450 <- FDb.InfiniumMethylation.hg19::get450k()
as.data.frame(hm450) %>% head()

    seqnames  start  end  width  strand  addressA  addressB  channel  platform  percentGC  sourceSeq  probeType  probeStart  probeEnd  probeTarget
cg04913815  chr16  60438  60439  2  *  24771476  ""  Both  HM450  0.58  TTTCGGTGGTACTGCGAAGGCAGAGCAGAGTTCTGCTCAGGTCAGACCCG  cg  60438  60487  60438
cg01686861  chr16  60748  60749  2  *  36644319  45624454  Red  HM450  0.76  CGCCCCCAGGCCGGCGCCGTGCGACTTTGCTCCTGCAACACACGCCCCCC  cg  60700  60749  60748
cg05558259  chr16  61085  61086  2  *  65765435  ""  Both  HM450  0.56  CAGCTAGGGACATTGCAGGCTCCTCTTGCTCAAAGTGTAGTGGCAGCACG  cg  61037  61086  61085
cg26978960  chr16  62460  62461  2  *  28717484  ""  Both  HM450  0.66  CGGCCCAGTAGAGCCCTAGGGGTGACGCCACTCCCACTCACTGTCGACTC  cg  62412  62461  62460
cg03792876  chr16  73243  73244  2  *  42725455  ""  Both  HM450  0.64  ATGGAGGCTTGGGCGGGTCACCCCCAGTGCAGGCCAAGATGCAGGTTACG  cg  73195  73244  73243
cg09699726  chr16  91602  91603  2  *  34629364  ""  Both  HM450  0.68  GCACTAGAGCCCCAGGGCCAGGGGAGACCCAGCATCCAAGGTGCACCACG  cg  91554  91603  91602

gene <- FDb.InfiniumMethylation.hg19::getNearestGene(hm450)
head(gene)
#            queryHits subjectHits distance nearestGeneSymbol
# cg04913815         1         666     1115          DDX11L10
# cg01686861         2         666      805          DDX11L10
# cg05558259         3         666      468          DDX11L10
# cg26978960         4         666        0          DDX11L10
# cg03792876         5         666     9152          DDX11L10
# cg09699726         6       14930     5375            POLR3K
transcript <- FDb.InfiniumMethylation.hg19::getNearestTranscript(hm450)
head(transcript)
#            queryHits subjectHits distance nearestGeneSymbol nearestTranscript
# cg04913815         1        1033     1115          DDX11L10        uc010bqm.2
# cg01686861         2        1033      805          DDX11L10        uc010bqm.2
# cg05558259         3        1033      468          DDX11L10        uc010bqm.2
# cg26978960         4        1033        0          DDX11L10        uc010bqm.2
# cg03792876         5        1033     9152          DDX11L10        uc010bqm.2
# cg09699726         6       40773     5375            POLR3K        uc002cfi.2
tss <- FDb.InfiniumMethylation.hg19::getNearestTSS(hm450)
head(tss)
#   queryHits subjectHits distance nearestGeneSymbol nearestTranscript
# cg04913815  1  799 1115   DDX11L10   uc010bqm.2
# cg01686861  2  799 805   DDX11L10   uc010bqm.2
# cg05558259  3  799 468   DDX11L10   uc010bqm.2
# cg26978960  4  799 904   DDX11L10   uc010bqm.2
# cg03792876  5  799 11687   DDX11L10   uc010bqm.2
# cg09699726  6   24097    12028     POLR3K   uc002cfi.2