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Update at Mon, Sep 09, 2019 10:25:11 PM

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jeroen committed Sep 9, 2019
1 parent c90af90 commit c157b602e3315345d1c5496cae4b732c9770b714
@@ -62,12 +62,12 @@ The error most likely occurred in:
>
> summary(res)
Query:
myeloma[ti] AND 2018/09/04[EDAT] : 2019/09/04[EDAT]
myeloma[ti] AND 2018/09/09[EDAT] : 2019/09/09[EDAT]

Result count: 1612>
Result count: 1602>
> fetch <- EUtilsGet(res)
Warning in file(con, "r") :
cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=31477451,31475039&retmode=xml': HTTP status was '429 Too Many Requests'
cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=31493537,31492570&retmode=xml': HTTP status was '429 Too Many Requests'
Error in file(con, "r") : cannot open the connection
Calls: EUtilsGet -> lapply -> FUN -> readLines -> file
Execution halted

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@@ -54,7 +54,7 @@ Last 13 lines of output:
== Failed ======================================================================
-- 1. Failure: traceback (@test-r-session.R#267) ------------------------------
`tb <- rs$traceback()` does not match "1: f() at ".
Actual value: "4: c(".handleSimpleError(function (e) ", "{", " {", " callr_data <- as.environment(\\"tools:callr\\")$`__callr_data__`", \n " err <- callr_data$err", " capture.output(assign(\\".Traceback\\", traceback(9), envir = baseenv()))", \n " dump.frames(\\"__callr_dump__\\")", " assign(\\".Last.dump\\", .GlobalEnv$`__callr_dump__`, envir = callr_data)", \n " rm(\\"__callr_dump__\\", envir = .GlobalEnv)", " calls <- sys.calls()", \n " dcframe <- which(vapply(calls, function(x) length(x) >= ", \n " 1 && identical(x[[1]], quote(do.call)), logical(1)))[1]", \n " if (!is.na(dcframe)) ", " e$`_ignore` <- list(c(1, dcframe + 1L))", \n " e$`_pid` <- Sys.getpid()", " e$`_timestamp` <- Sys.time()", \n " e <- err$add_trace_back(e)", " saveRDS(list(\\"error\\", e), file = paste0(\\"C:\\\\\\\\rtools40\\\\\\\\tmp\\\\\\\\Rtmp8itFRC\\\\\\\\file113041093df2\\", ", \n " \\".error\\"))", " }", "}, \\"oops\\", base::quote(g()))"\n )\n3: "stop(\\"oops\\")"\n2: "g()"\n1: "f()""
Actual value: "4: c(".handleSimpleError(function (e) ", "{", " {", " callr_data <- as.environment(\\"tools:callr\\")$`__callr_data__`", \n " err <- callr_data$err", " capture.output(assign(\\".Traceback\\", traceback(9), envir = baseenv()))", \n " dump.frames(\\"__callr_dump__\\")", " assign(\\".Last.dump\\", .GlobalEnv$`__callr_dump__`, envir = callr_data)", \n " rm(\\"__callr_dump__\\", envir = .GlobalEnv)", " calls <- sys.calls()", \n " dcframe <- which(vapply(calls, function(x) length(x) >= ", \n " 1 && identical(x[[1]], quote(do.call)), logical(1)))[1]", \n " if (!is.na(dcframe)) ", " e$`_ignore` <- list(c(1, dcframe + 1L))", \n " e$`_pid` <- Sys.getpid()", " e$`_timestamp` <- Sys.time()", \n " e <- err$add_trace_back(e)", " saveRDS(list(\\"error\\", e), file = paste0(\\"C:\\\\\\\\rtools40\\\\\\\\tmp\\\\\\\\RtmpQjUlQc\\\\\\\\file135844d2c77\\", ", \n " \\".error\\"))", " }", "}, \\"oops\\", base::quote(g()))"\n )\n3: "stop(\\"oops\\")"\n2: "g()"\n1: "f()""

-- 2. Failure: traceback (@test-r-session.R#268) ------------------------------
c(tb[[4]]) not equal to "f()".

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@@ -24,9 +24,9 @@ while read -r PKG; do
LOGLINE=$(grep "Status: " $LOGFILE)
echo "Previous result for $PKG: $LOGLINE"
if echo $LOGLINE | grep -Pq 'Status: (OK|[0-9]+ (NOTE|WARN))'; then
#echo "SKIPPING $PKG"
#continue
echo "Retrying..."
echo "SKIPPING $PKG"
continue
#echo "Retrying..."
fi
fi
if [ $(grep "^$PKG\\W*$" DoNotCheck) ] || [ $(grep "^$PKG\\W*$" DoNotCompile) ]; then

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