Last updated on 2026-07-23 02:51:05 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.2 | 19.04 | 175.31 | 194.35 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.9.2 | 13.19 | 130.76 | 143.95 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.9.2 | 30.00 | 271.05 | 301.05 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.9.2 | 12.00 | 121.62 | 133.62 | OK | |
| r-devel-windows-x86_64 | 0.9.2 | 20.00 | 159.00 | 179.00 | OK | |
| r-patched-linux-x86_64 | 0.9.2 | 18.15 | 169.62 | 187.77 | OK | |
| r-release-linux-x86_64 | 0.9.2 | 17.11 | 169.58 | 186.69 | OK | |
| r-release-macos-arm64 | 0.9.2 | 5.00 | 45.00 | 50.00 | OK | |
| r-release-macos-x86_64 | 0.9.2 | 13.00 | 179.00 | 192.00 | OK | |
| r-release-windows-x86_64 | 0.9.2 | 21.00 | 161.00 | 182.00 | OK | |
| r-oldrel-macos-arm64 | 0.9.2 | OK | ||||
| r-oldrel-macos-x86_64 | 0.9.2 | 12.00 | 194.00 | 206.00 | OK | |
| r-oldrel-windows-x86_64 | 0.9.2 | 27.00 | 216.00 | 243.00 | OK |
Version: 0.9.2
Check: tests
Result: ERROR
Running ‘test-01-cipher.R’ [4s/5s]
Running ‘test-02-seqclus.R’ [4s/6s]
Running ‘test-04-sg.R’ [5s/7s]
Running ‘test-05-words.R’ [4s/5s]
Running the tests in ‘tests/test-01-cipher.R’ failed.
Complete output:
> library(SVAlignR)
>
> motif <- "0-50-74-0-50-74-25-26-35"
> alfa <- Cipher(motif)
> alfa
An object of class "Cipher"
Slot "forward":
0 25 26 35 50 74
"A" "B" "C" "D" "E" "F"
Slot "reverse":
A B C D E F - ?
"0" "25" "26" "35" "50" "74" ":" "?"
Slot "bytes":
[1] 1
>
> en <-encode(alfa, motif)
> en
[1] "AEFAEFBCD"
>
> de <- decode(alfa, en)
> de
[1] "0-50-74-0-50-74-25-26-35"
> de == motif
[1] TRUE
>
> ## bad Cipher inputs
> try( Cipher(13) )
Error in strsplit(sampleText, split) : non-character argument
> try( Cipher(motif, extras = 13) )
Error in Cipher(motif, extras = 13) :
All elements of 'extras' must have names.
> try( Cipher(motif, extras = c(z = "zero", 13)) )
Error in Cipher(motif, extras = c(z = "zero", 13)) :
All elements of 'extras' must have names.
> try( Cipher(motif, extras = c(A = "zero")) )
Error in Cipher(motif, extras = c(A = "zero")) :
Names of 'extras' cannot include symbols in 'sampleText'.
> try( Cipher(motif, extras = c("x" = 26)) )
Error in Cipher(motif, extras = c(x = 26)) :
Values of 'extras' cannot match letter in the 'forward' cipher.
>
> odd <- c(motif, "0-0-50-74-61")
> try( encode(alfa, odd) )
Error in .xlate(text, cipher@forward, "\\-", "", 1) :
Text includes unknown characters: 61
> try( encode(odd, alfa) )
Error in strsplit(txt, split) : non-character argument
>
> ## Longer alphabets
> nchar(IT <- intToUtf8(L <- c(38:44, 46:57, 59:62, 64:126)))
[1] 86
> ## omit hyphen, colon, and question
> JT <- paste(strsplit(IT, "|")[[1]], collapse = "-")
> gamma <- Cipher(JT)
Warning message:
In Cipher(JT) :*** buffer overflow detected ***: terminated
Aborted
Running the tests in ‘tests/test-02-seqclus.R’ failed.
Complete output:
> library(SVAlignR)
> data(longreads)
> N <- 32
> sequences <- longreads$connection[1:N]
>
> # specify Levenshtein (should get two warnings)
> sc1 <- SequenceCluster(sequences, method = "levenshtein", NC = 4)
Warning messages:
1: In SequenceCluster(sequences, method = "levenshtein", NC = 4) :
Adding names to input sequences.
2: In SequenceCluster(sequences, method = "levenshtein", NC = 4) :
Removing 6 duplicated sequences.
> plot(sc1@hc)
>
> # after assigning names, should get one warning
> names(sequences) <- rownames(longreads)[1:N]
> sc1 <- SequenceCluster(sequences, method = "levenshtein", NC = 4)
Warning message:
In SequenceCluster(sequences, method = "levenshtein", NC = 4) :*** buffer overflow detected ***: terminated
Aborted
Running the tests in ‘tests/test-05-words.R’ failed.
Complete output:
> library(SVAlignR)
>
> ## single byte
> data(longreads)
> raw <- longreads$connection
> alfa <- Cipher(raw)
> coded <- encode(alfa, raw)
> makeWords(coded, 3)
AAA AAD AAE AAb ADA ADY AEA AFK AKH AKN ALN APR AbB AbU Abd Abg Abm Abo Abq Afq
55 14 1 26 18 1 1 4 1 13 4 6 3 11 1 1 1 1 95 1
Ahq Ajq Alq Anq Ass BrA Bss DAA DAD DAb EAA FKN GAb IAb KNM KNq LNq MNq NMN NqA
1 2 1 2 1 1 1 9 2 5 1 3 1 2 6 11 3 4 6 11
Nqk Nss OqP PRA PRc QqP RAA RAC RAP RAb RAf RAn Rcq STA TAb Tsb UVA UaA VAD WAA
20 1 3 54 6 1 2 2 1 38 2 2 6 4 4 1 1 1 1 1
aAA aAZ bBr bBs bUV bUa bdq bgA bmA bpb bqA bqG bqP bqS bqb bqe bqk cqP dqP eqP
12 1 1 1 1 1 2 1 1 1 71 1 15 8 5 8 4 6 3 10
fqP gAb hqA iQq jqA jqk kqA kqk lqA mAb nqP pbq qAA qAF qAK qAL qAP qAb qAj qAl
1 1 1 1 1 1 21 6 1 1 2 1 19 3 23 3 3 44 6 1
qAs qGA qPR qST qbq qeq qkq qks rAA sAb sAs sFK sNq sNs sTs sbq ssA ssF ssN sss
1 1 51 6 8 9 29 1 1 1 1 1 1 1 1 1 1 1 2 1
> countWords(coded, 3)
AAA AAD AAE AAb ADA ADY AEA AFK AKH AKN ALN APR AbB AbU Abd Abg Abm Abo Abq Afq
55 14 1 26 18 1 1 4 1 13 4 6 3 11 1 1 1 1 95 1
Ahq Ajq Alq Anq Ass BrA Bss DAA DAD DAb EAA FKN GAb IAb KNM KNq LNq MNq NMN NqA
1 2 1 2 1 1 1 9 2 5 1 3 1 2 6 11 3 4 6 11
Nqk Nss OqP PRA PRc QqP RAA RAC RAP RAb RAf RAn Rcq STA TAb Tsb UVA UaA VAD WAA
20 1 3 54 6 1 2 2 1 38 2 2 6 4 4 1 1 1 1 1
aAA aAZ bBr bBs bUV bUa bdq bgA bmA bpb bqA bqG bqP bqS bqb bqe bqk cqP dqP eqP
12 1 1 1 1 1 2 1 1 1 71 1 15 8 5 8 4 6 3 10
fqP gAb hqA iQq jqA jqk kqA kqk lqA mAb nqP pbq qAA qAF qAK qAL qAP qAb qAj qAl
1 1 1 1 1 1 21 6 1 1 2 1 19 3 23 3 3 44 6 1
qAs qGA qPR qST qbq qeq qkq qks rAA sAb sAs sFK sNq sNs sTs sbq ssA ssF ssN sss
1 1 51 6 8 9 29 1 1 1 1 1 1 1 1 1 1 1 2 1
> countWords(coded, 3, alfa)
0-0-0 0-0-14 0-0-15 0-0-50 0-14-0 0-14-45 0-15-0 0-17-25
55 14 1 26 18 1 1 4
0-25-23 0-25-28 0-26-28 0-32-34 0-50-12 0-50-37 0-50-52 0-50-57
1 13 4 6 3 11 1 1
0-50-65 0-50-70 0-50-74 0-56-74 0-58-74 0-60-74 0-63-74 0-66-74
1 1 95 1 1 2 1 2
0-x-x 12-75-0 12-x-x 14-0-0 14-0-14 14-0-50 15-0-0 17-25-28
1 1 1 9 2 5 1 3
19-0-50 24-0-50 25-28-27 25-28-74 26-28-74 27-28-74 28-27-28 28-74-0
1 2 6 11 3 4 6 11
28-74-61 28-x-x 31-74-32 32-34-0 32-34-51 33-74-32 34-0-0 34-0-13
20 1 3 54 6 1 2 2
34-0-32 34-0-50 34-0-56 34-0-66 34-51-74 35-36-0 36-0-50 36-x-50
1 38 2 2 6 4 4 1
37-38-0 37-48-0 38-0-14 40-0-0 48-0-0 48-0-46 50-12-75 50-12-x
1 1 1 1 12 1 1 1
50-37-38 50-37-48 50-52-74 50-57-0 50-65-0 50-71-50 50-74-0 50-74-19
1 1 2 1 1 1 71 1
50-74-32 50-74-35 50-74-50 50-74-54 50-74-61 51-74-32 52-74-32 54-74-32
15 8 5 8 4 6 3 10
56-74-32 57-0-50 58-74-0 6-33-74 60-74-0 60-74-61 61-74-0 61-74-61
1 1 1 1 1 1 21 6
63-74-0 65-0-50 66-74-32 71-50-74 74-0-0 74-0-17 74-0-25 74-0-26
1 1 2 1 19 3 23 3
74-0-32 74-0-50 74-0-60 74-0-63 74-0-x 74-19-0 74-32-34 74-35-36
3 44 6 1 1 1 51 6
74-50-74 74-54-74 74-61-74 74-61-x 75-0-0 x-0-50 x-0-x x-17-25
8 9 29 1 1 1 1 1
x-28-74 x-28-x x-36-x x-50-74 x-x-0 x-x-17 x-x-28 x-x-x
1 1 1 1 1 1 2 1
>
> IT <- intToUtf8(L <- c(38:44, 46:57, 59:62, 64:126)) ## omit hyphen, colon, and question
> JT <- paste(strsplit(IT, "|")[[1]], collapse = "-")
> beta <- Cipher(JT)
Warning message:
In Cipher(JT) :*** buffer overflow detected ***: terminated
Aborted
Flavor: r-devel-linux-x86_64-debian-gcc