Last updated on 2020-02-19 10:49:02 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 15.14 | 134.10 | 149.24 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 15.06 | 102.41 | 117.47 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 178.03 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 175.72 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.1.0 | 27.00 | 121.00 | 148.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.1.0 | 42.00 | 176.00 | 218.00 | NOTE | |
| r-patched-linux-x86_64 | 1.1.0 | 13.16 | 109.11 | 122.27 | NOTE | |
| r-patched-solaris-x86 | 1.1.0 | 221.70 | NOTE | |||
| r-release-linux-x86_64 | 1.1.0 | 14.85 | 109.41 | 124.26 | NOTE | |
| r-release-windows-ix86+x86_64 | 1.1.0 | 29.00 | 120.00 | 149.00 | NOTE | |
| r-release-osx-x86_64 | 1.1.0 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 1.1.0 | 11.00 | 99.00 | 110.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.1.0 | NOTE |
Version: 1.1.0
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Title field: should not end in a period.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in 'PepPrep-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compHomToPepFasta
> ### Title: Comparison of proteins and creating homologous peptides workflow
> ### Aliases: compHomToPepFasta
>
> ### ** Examples
>
> #load data and set arguments
>
> #Uniprot proteom FASTA databases
> #(just a small example with two proteins each)
> path_o1 <- system.file("extdata", "ExampleHumanProt.fasta", package="PepPrep")
> path_o2 <- system.file("extdata", "ExampleMouseProt.fasta", package="PepPrep")
>
> #where to write the result and how to formate
> path <- paste0(getwd(), "/myTest_compHomToPep.fasta")
> width <- 60
>
> #call workflow
> test <- compHomToPepFasta(path_o1, path_o2, path, width)
[1] "start findEntryPairs"
[1] "start addHeader"
[1] "start addAllPeptides"
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PepPrep
--- call from context ---
trypsinateSeq(ooseq, target, exception)
--- call from argument ---
if (class(tryppos) == "integer") {
if (length(tryppos) == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
else {
tryppos <- matrix(c(tryppos["start"], tryppos["end"]),
nrow = 1, ncol = 2, dimnames = list(c(), c("start",
"end")))
}
}
--- R stacktrace ---
where 1: trypsinateSeq(ooseq, target, exception)
where 2: addAllPeptides(tbl, path_o1, path_o2, target, exception)
where 3: compHomToPepFasta(path_o1, path_o2, path, width)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (seq, target = "K|R", exception = "P")
{
targettest <- regexpr("^[ARNDCQEGHILKMFPSTWYV]([|][ARNDCQEGHILKMFPSTWYV])*",
target)
exceptiontest <- regexpr("^[ARNDCQEGHILKMFPSTWYV]([|][ARNDCQEGHILKMFPSTWYV])*",
exception)
if (attr(targettest, "match.length") != nchar(target)) {
message <- "trypsinateSeq: Error target is wrong"
print(message)
return(message)
}
if (attr(exceptiontest, "match.length") != nchar(exception)) {
message <- "trypsinateSeq: Error exception is wrong"
print(message)
return(message)
}
vrk <- str_locate_all(seq, target)[[1]]
vp <- str_locate_all(seq, exception)[[1]]
pminus <- vp - 1
tryppos <- vrk[!(vrk[, 1] %in% pminus[, 1]), ]
if (class(tryppos) == "integer") {
if (length(tryppos) == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
else {
tryppos <- matrix(c(tryppos["start"], tryppos["end"]),
nrow = 1, ncol = 2, dimnames = list(c(), c("start",
"end")))
}
}
if (class(tryppos) == "matrix") {
if (dim(tryppos)[1] == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
}
result <- rep("", length(tryppos[, 1]) + 1)
first <- 1
for (i in seq(along = tryppos[, 1])) {
last <- tryppos[i, 1]
pep <- substr(seq, first, last)
result[i] <- pep
first <- last + 1
}
last <- nchar(seq)
if (first <= last) {
result[length(result)] <- substr(seq, first, last)
}
return(result)
}
<bytecode: 0xa4cdc10>
<environment: namespace:PepPrep>
--- function search by body ---
Function trypsinateSeq in namespace PepPrep has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(tryppos) == "integer") { :
the condition has length > 1
Calls: compHomToPepFasta -> addAllPeptides -> trypsinateSeq
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘PepPrep-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compHomToPepFasta
> ### Title: Comparison of proteins and creating homologous peptides workflow
> ### Aliases: compHomToPepFasta
>
> ### ** Examples
>
> #load data and set arguments
>
> #Uniprot proteom FASTA databases
> #(just a small example with two proteins each)
> path_o1 <- system.file("extdata", "ExampleHumanProt.fasta", package="PepPrep")
> path_o2 <- system.file("extdata", "ExampleMouseProt.fasta", package="PepPrep")
>
> #where to write the result and how to formate
> path <- paste0(getwd(), "/myTest_compHomToPep.fasta")
> width <- 60
>
> #call workflow
> test <- compHomToPepFasta(path_o1, path_o2, path, width)
[1] "start findEntryPairs"
[1] "start addHeader"
[1] "start addAllPeptides"
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PepPrep
--- call from context ---
trypsinateSeq(ooseq, target, exception)
--- call from argument ---
if (class(tryppos) == "integer") {
if (length(tryppos) == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
else {
tryppos <- matrix(c(tryppos["start"], tryppos["end"]),
nrow = 1, ncol = 2, dimnames = list(c(), c("start",
"end")))
}
}
--- R stacktrace ---
where 1: trypsinateSeq(ooseq, target, exception)
where 2: addAllPeptides(tbl, path_o1, path_o2, target, exception)
where 3: compHomToPepFasta(path_o1, path_o2, path, width)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (seq, target = "K|R", exception = "P")
{
targettest <- regexpr("^[ARNDCQEGHILKMFPSTWYV]([|][ARNDCQEGHILKMFPSTWYV])*",
target)
exceptiontest <- regexpr("^[ARNDCQEGHILKMFPSTWYV]([|][ARNDCQEGHILKMFPSTWYV])*",
exception)
if (attr(targettest, "match.length") != nchar(target)) {
message <- "trypsinateSeq: Error target is wrong"
print(message)
return(message)
}
if (attr(exceptiontest, "match.length") != nchar(exception)) {
message <- "trypsinateSeq: Error exception is wrong"
print(message)
return(message)
}
vrk <- str_locate_all(seq, target)[[1]]
vp <- str_locate_all(seq, exception)[[1]]
pminus <- vp - 1
tryppos <- vrk[!(vrk[, 1] %in% pminus[, 1]), ]
if (class(tryppos) == "integer") {
if (length(tryppos) == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
else {
tryppos <- matrix(c(tryppos["start"], tryppos["end"]),
nrow = 1, ncol = 2, dimnames = list(c(), c("start",
"end")))
}
}
if (class(tryppos) == "matrix") {
if (dim(tryppos)[1] == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
}
result <- rep("", length(tryppos[, 1]) + 1)
first <- 1
for (i in seq(along = tryppos[, 1])) {
last <- tryppos[i, 1]
pep <- substr(seq, first, last)
result[i] <- pep
first <- last + 1
}
last <- nchar(seq)
if (first <= last) {
result[length(result)] <- substr(seq, first, last)
}
return(result)
}
<bytecode: 0x5633063a4af8>
<environment: namespace:PepPrep>
--- function search by body ---
Function trypsinateSeq in namespace PepPrep has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(tryppos) == "integer") { :
the condition has length > 1
Calls: compHomToPepFasta -> addAllPeptides -> trypsinateSeq
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘PepPrep-Ex.R’ failed
The error most likely occurred in:
> ### Name: compHomToPepFasta
> ### Title: Comparison of proteins and creating homologous peptides workflow
> ### Aliases: compHomToPepFasta
>
> ### ** Examples
>
> #load data and set arguments
>
> #Uniprot proteom FASTA databases
> #(just a small example with two proteins each)
> path_o1 <- system.file("extdata", "ExampleHumanProt.fasta", package="PepPrep")
> path_o2 <- system.file("extdata", "ExampleMouseProt.fasta", package="PepPrep")
>
> #where to write the result and how to formate
> path <- paste0(getwd(), "/myTest_compHomToPep.fasta")
> width <- 60
>
> #call workflow
> test <- compHomToPepFasta(path_o1, path_o2, path, width)
[1] "start findEntryPairs"
[1] "start addHeader"
[1] "start addAllPeptides"
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PepPrep
--- call from context ---
trypsinateSeq(ooseq, target, exception)
--- call from argument ---
if (class(tryppos) == "integer") {
if (length(tryppos) == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
else {
tryppos <- matrix(c(tryppos["start"], tryppos["end"]),
nrow = 1, ncol = 2, dimnames = list(c(), c("start",
"end")))
}
}
--- R stacktrace ---
where 1: trypsinateSeq(ooseq, target, exception)
where 2: addAllPeptides(tbl, path_o1, path_o2, target, exception)
where 3: compHomToPepFasta(path_o1, path_o2, path, width)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (seq, target = "K|R", exception = "P")
{
targettest <- regexpr("^[ARNDCQEGHILKMFPSTWYV]([|][ARNDCQEGHILKMFPSTWYV])*",
target)
exceptiontest <- regexpr("^[ARNDCQEGHILKMFPSTWYV]([|][ARNDCQEGHILKMFPSTWYV])*",
exception)
if (attr(targettest, "match.length") != nchar(target)) {
message <- "trypsinateSeq: Error target is wrong"
print(message)
return(message)
}
if (attr(exceptiontest, "match.length") != nchar(exception)) {
message <- "trypsinateSeq: Error exception is wrong"
print(message)
return(message)
}
vrk <- str_locate_all(seq, target)[[1]]
vp <- str_locate_all(seq, exception)[[1]]
pminus <- vp - 1
tryppos <- vrk[!(vrk[, 1] %in% pminus[, 1]), ]
if (class(tryppos) == "integer") {
if (length(tryppos) == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
else {
tryppos <- matrix(c(tryppos["start"], tryppos["end"]),
nrow = 1, ncol = 2, dimnames = list(c(), c("start",
"end")))
}
}
if (class(tryppos) == "matrix") {
if (dim(tryppos)[1] == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
}
result <- rep("", length(tryppos[, 1]) + 1)
first <- 1
for (i in seq(along = tryppos[, 1])) {
last <- tryppos[i, 1]
pep <- substr(seq, first, last)
result[i] <- pep
first <- last + 1
}
last <- nchar(seq)
if (first <= last) {
result[length(result)] <- substr(seq, first, last)
}
return(result)
}
<bytecode: 0xb8859a0>
<environment: namespace:PepPrep>
--- function search by body ---
Function trypsinateSeq in namespace PepPrep has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(tryppos) == "integer") { :
the condition has length > 1
Calls: compHomToPepFasta -> addAllPeptides -> trypsinateSeq
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘PepPrep-Ex.R’ failed
The error most likely occurred in:
> ### Name: compHomToPepFasta
> ### Title: Comparison of proteins and creating homologous peptides workflow
> ### Aliases: compHomToPepFasta
>
> ### ** Examples
>
> #load data and set arguments
>
> #Uniprot proteom FASTA databases
> #(just a small example with two proteins each)
> path_o1 <- system.file("extdata", "ExampleHumanProt.fasta", package="PepPrep")
> path_o2 <- system.file("extdata", "ExampleMouseProt.fasta", package="PepPrep")
>
> #where to write the result and how to formate
> path <- paste0(getwd(), "/myTest_compHomToPep.fasta")
> width <- 60
>
> #call workflow
> test <- compHomToPepFasta(path_o1, path_o2, path, width)
[1] "start findEntryPairs"
[1] "start addHeader"
[1] "start addAllPeptides"
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PepPrep
--- call from context ---
trypsinateSeq(ooseq, target, exception)
--- call from argument ---
if (class(tryppos) == "integer") {
if (length(tryppos) == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
else {
tryppos <- matrix(c(tryppos["start"], tryppos["end"]),
nrow = 1, ncol = 2, dimnames = list(c(), c("start",
"end")))
}
}
--- R stacktrace ---
where 1: trypsinateSeq(ooseq, target, exception)
where 2: addAllPeptides(tbl, path_o1, path_o2, target, exception)
where 3: compHomToPepFasta(path_o1, path_o2, path, width)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (seq, target = "K|R", exception = "P")
{
targettest <- regexpr("^[ARNDCQEGHILKMFPSTWYV]([|][ARNDCQEGHILKMFPSTWYV])*",
target)
exceptiontest <- regexpr("^[ARNDCQEGHILKMFPSTWYV]([|][ARNDCQEGHILKMFPSTWYV])*",
exception)
if (attr(targettest, "match.length") != nchar(target)) {
message <- "trypsinateSeq: Error target is wrong"
print(message)
return(message)
}
if (attr(exceptiontest, "match.length") != nchar(exception)) {
message <- "trypsinateSeq: Error exception is wrong"
print(message)
return(message)
}
vrk <- str_locate_all(seq, target)[[1]]
vp <- str_locate_all(seq, exception)[[1]]
pminus <- vp - 1
tryppos <- vrk[!(vrk[, 1] %in% pminus[, 1]), ]
if (class(tryppos) == "integer") {
if (length(tryppos) == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
else {
tryppos <- matrix(c(tryppos["start"], tryppos["end"]),
nrow = 1, ncol = 2, dimnames = list(c(), c("start",
"end")))
}
}
if (class(tryppos) == "matrix") {
if (dim(tryppos)[1] == 0) {
tryppos <- matrix(c(1, nchar(seq)), nrow = 1, ncol = 2,
dimnames = list(c(), c("start", "end")))
}
}
result <- rep("", length(tryppos[, 1]) + 1)
first <- 1
for (i in seq(along = tryppos[, 1])) {
last <- tryppos[i, 1]
pep <- substr(seq, first, last)
result[i] <- pep
first <- last + 1
}
last <- nchar(seq)
if (first <= last) {
result[length(result)] <- substr(seq, first, last)
}
return(result)
}
<bytecode: 0xb5b4d28>
<environment: namespace:PepPrep>
--- function search by body ---
Function trypsinateSeq in namespace PepPrep has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(tryppos) == "integer") { :
the condition has length > 1
Calls: compHomToPepFasta -> addAllPeptides -> trypsinateSeq
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: package ‘biomaRt’ was built under R version 3.6.1
Flavor: r-release-osx-x86_64