Tag Archives: error

PHP update issues: Goodby miniflux, welcome freshRSS

With a forced upgrade of my provider from PHP 7.4 to PHP 8.1  miniflux v1  did not work anymore with Reeder 5. After trying to  correct all issues with phan, I decided to switch to a freshRSS install that has even a more modern Google API.

BTW I find it quite helpful to debug PHP 7.4 code by intentional throwing a javascript error to block any ongoing action with

throw "SimulatedException"

and setting PHP more verbose with

error_reporting(E_ALL | E_STRICT)

While it was quite straightforward to replace all “each” with “for each”, or “read_exif_date” with “exif_read_date” the main issue were unquoted “$_SERVER” variables and functions that need to be checked for missing variables

$rows= (is_countable($ret) ? count($ret) : 0

The biggest problems came by Nextcloud update to version 25. It turns out that there is a file limit of 262.144 of my internet provider.

Any Nextcloud update always needs about 30.000 files. Whenever it encounters any other error, a restart produces  another 30.000 files, basically killing my account.

In contrast to the documentation the issue is also not at the root nextcloud updater directory but in the data directory.

superfluous Nextcloud backup files hiding in the data directory

Nature Genetics corrupted by 23andme

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Track down the “no object… error in post.php”

Recently I encountered this strange error message in WordPress when trying to write a new post. Maybe I haven’t done any major changes, only removed a security plugin recently while the whole system is continuously updated.

Disabling all plugins and reverting to the standard twentyfifteen theme did not help. Inspection of post.php also did not show anything unusual (the indicated line number was probably wrong due to several includes). Googling the error message also did not help as these lead only to site specific problems. Continue reading Track down the “no object… error in post.php”

The true reason for retractions?

Retractions are increasing anytime I look around retraction watch. A new PNAS paper now has the most thorough analysis of retractions:

A detailed review of all 2,047 biomedical and life-science research articles indexed by PubMed as retracted on May 3, 2012 revealed that only 21.3% of retractions were attributable to error. In contrast, 67.4% of retractions were attributable to misconduct, including fraud or suspected fraud (43.4%), duplicate publication (14.2%), and plagiarism (9.8%) …fraud has increased ∼10-fold since 1975.

So, fraud is the most frequent cause – and it usually does not come isolated Continue reading The true reason for retractions?

An enormous step forward in whole genome sequencing

The idea might not be new – we already diluted DNA already a decade ago ( see this 2003 paper ). A new Nature paper by Peters ( Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells… ) now shows that diluting DNA into 384 wells, adding unique tags, and pooling again before sequencing everything on a Hiseq, will result in an enormous reduction of sequencing errors – a problem that we are fighting now for a year. IMHO the paper isn’t primarily about the low number of cells that can be sequenced, but also about error reduction in WGS. The two key facts are certainly

To ensure complete representation of the genome we maximized the input of DNA fragments for a given read coverage and number of aliquots. Unlike other experimental approaches this resulted in low- coverage read data for each fragment in each of the wells a fragment is found in.

plus an intelligent phasing algorithm Continue reading An enormous step forward in whole genome sequencing

PLINK: Bug or feature?

I am struggling now for 4 weeks with some unusual behaviour in PLINK that gives me different results with a trait of the alternate phenotype files either by calling that trait directly

plink –file mydata –tdt –pheno pheno2.txt –mpheno 1

or from a loop over all traits

plink –file mydata –tdt –pheno pheno2.txt –all-pheno

It seems that I am working with different numbers at both occasions – click to enlarge the log Continue reading PLINK: Bug or feature?

Errare humanum est

All4quotes and becontent have (mainly German) quotes. My all time favorites are

Aurelius Augustinus: Irren ist menschlich, aber aus Leidenschaft im Irrtum zu verharren, ist teuflisch.

August von Kotzebue: Menschen irren, aber nur große Menschen erkennen ihren Irrtum.

Christian Friedrich Hebbel: Die Menschheit läßt sich keinen Irrtum nehmen, der ihr nützt.

Friedrich von Schiller: Liegt der Irrtum nur erst, wie ein Grundstein, unter dem Boden, immer baut man darauf, nimmermehr kömmt er an den Tag.

Friedrich von Schiller: Hundertmal wer ich’s euch sagen und tausendmal: Irrtum ist Irrtum! Ob ihn der größte Mann, ob ihn der kleinste beging.

Georg Christoph Lichtenberg: Nur der Betrug entehrt, der Irrtum nie.
Continue reading Errare humanum est